Forsaken Future
by LittleKnux2008
Summary: After months of imprisonment, Rodney McKay returns to Atlantis, only to find that everything changed...for the worse.
1. one

**Author's Note: **This is the sequel to a songfic I wrote a while ago called "Cold". You can find it at my homepage under Ficlets And Songfics. The characters, setting, terms, etc don't belong to me. **This story contains violent images, torture, and nonconsensual sex.** If you are offended by any of these things, turn back now. That aside, I hope you guys enjoy this piece and please review!

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Major John Sheppard warily glanced back at his team as they entered the Genii facility. It had been six months to the day that Rodney McKay had disappeared. Six long months… John wondered how they had made it through the siege without Rodney on their side. As soon as the siege was over, Elizabeth Weir had ordered all teams on a search and rescue. Remembering the hollow pain in his chest every time that they returned from a planet without Rodney, John winced. If only he'd been paying more attention on Choc; if only he had noticed Rodney slip away from the group…then perhaps Rodney would have been with them, not enduring God-knows-what at the hands of the Genii. Three months ago, Elizabeth had no choice but to declare Rodney missing, presumed dead. Still, she kept rotating teams to search the planets in the Pegasus Galaxy not already searched in the empty hope that they would find Rodney. Since about a month ago, no more teams left Atlantis with the primary mission to find Rodney McKay.

Until today. John noted the apprehension on both Lieutenant Ford and Teyla's faces before turning away, eyes quickly adjusting to the darkness of the building. He didn't blame the two – who knew what they would find? The tip that this might be the place where Rodney was being kept had come a week ago, through Sora – formerly of the Genii. After months in Atlantis, she had turned her back on the Genii and pledged herself to Atlantis. She was regarded with suspicion for quite some time, but she had proved herself. A few weeks ago, she had been sent back to the Genii home world as a spy. A week ago, she had reported back with this news. Sheppard, Ford, and Teyla had gone to the Genii planet. Sora cleared the entrance to the underground layer of guards and the like, making it simple for the three to get into the underground city. Now, here they were, in a prison on the far outskirts of the dark city.

John turned to face his team once more. His back was against a wall – something squishy, the origins of which he didn't wish to ponder, pressing into him. To his left was a long hallway, several groups of bars visible. The metallic stench of blood reached John's nostrils, adding to a growing feeling of uneasiness. "Recon first," he told the two in a quiet order, nodding to the Wraith stunners they carried with them, "Stun all the guards you see; don't shoot to kill unless you have to." John caught Ford's eye, and he hesitated. "No matter what you see, don't stop," he told them, "Keep going; look straight ahead." Teyla and Ford both nodded. Teyla went first, her steps graceful and quiet as she headed down the hallway, her keen eyes on the shadows. Aiden followed her, staying to the right side of the hallway, his body covered in shadows. Behind Ford, Sheppard did the same. One lone woman would look a lot less threatening than a group of three.

Aiden rearranged his grip on the Wraith stunner, nervously looking from left to right, careful not to look into any cells. What had the Genii done to McKay? Aiden's eyes inadvertently focused beyond the bars of one cell. Immediately, he felt his body unable to move. Inside the cell lay a little girl, not more than the age of eight. She was sitting with her back against the wall, her head titled toward the ceiling. But that was where all normalcies ended and the terrifying reality of the Genii cruelty began. Blood, previously running from a long cut across her forehead, had dried across her innocent face. Her hair had matted and tangled, the blood and dirt in her hair making it nearly impossible to tell her hair color. The young girl's left arm hung at a haphazard angle, and, his eyes moving lower, a part of her fractured ulna had broken through the skin on her forearm. Continuing his study with bile rising quickly to his mouth, Aiden saw that she only had three twisted fingers, scabbed joints remaining where her thumb and pinky had been. She sat in a pool of thick, crimson blood – Aiden didn't dare think about where the blood had come from. Had the Genii torture really gone so far? He forced himself to swallow, as thick as his throat was becoming. She was just a girl! Hot, burning hatred for the Genii rushed through his veins. But she was a female in a prison with no regulations. Aiden's hands tightened on the stunner. Her chest had long since stopped moving with breath.

"Lieutenant," he heard Sheppard's voice as if it was coming from a distance before feeling a pressure on his shoulder.

"Major…" Aiden's voice trailed off during the word, his gaze not leaving the young girl.

"I know," John said softly, his eyes, too, trained on the cell.

"If they did this to a little girl…" Aiden trailed off, the words weighing heavily on his mind unspoken. They did not need to be. What had the Genii done to Rodney?

"I know," John repeated firmly, "but we have to keep moving." With a jolt, Aiden realized that Teyla had turned down another hallway. He nodded, and focused again on the mission, pushing away the horrifying image of the dead girl. John glanced back at the cell once more before trailing Aiden.

Ten minutes later, they had stunned five guards and knew the layout of the prison. John had a nagging suspicion that, though called a prison by the Genii it was far from one and simply seemed to serve as a torture house. There were three hallways, connected in a 'U', the third hallway leading to a dead end where they had moved the bodies of the guards.

"All right," John glanced at the guards for a moment before addressing his team. His team seemed so small without McKay. _'And his ego,' _John thought. The inward joke which would've once led to a smirk on his face, led only to a hollow twinge within him. "Teyla, you search this hallway, I'll search the first one, and Ford will take the middle one. Count how many cells and how many dead. If we can, I want to transfer the living prisoners to our holding cells. At least they can be taken care of while we judge whether they should be in prison or not," John told them. He hesitated for the briefest moment before plunging onward. "I guarantee you that Rodney will not look the same. Look carefully."

As he walked to his hallway, John wished he could have done this alone. Ford and Teyla didn't need to see this; this torture, this destruction. It aged you in a way the Wraith could not. It aged your soul; your mind. John glanced into the first cell that moved into view as he walked into his hallway, swallowing at the gruesome sight that awaited them. Was Rodney – _'No,'_ John thought firmly, pushing the thought out of his head, _'There's always hope.'_ And there was hope now.

However dim it was.

---

Fourteen cells: twelve dead and two barely hanging on. John thought of the statistics of his hallway grimly as he moved to the fifteenth cell. He stared into it, bracing himself for another ghastly sight. John was not let down. There was enough dim light in the cell not to need his flashlight. The form of a man was pressed against a wall. His clothing was torn, the skin it revealed badly bruised. There seemed to be dried blood everywhere on his body – but John spotted brighter red liquid against it and he felt hope that this one was alive. John spotted some blood stained, frayed bandages around various places, but they had long since passed their use, if they ever fulfilled it. The man's legs were stretched out in front of him, and John could see the extensive damage to the kneecaps from where he stood. They appeared to be shattered, and the man's left foot was twisted in a way it simply wasn't meant to be twisted. On top of it all, the man was terrifyingly thin. John waited for the chest to move with a breath, and to his surprise, it did. Slowly, with a rasping noise, but nonetheless his chest rose and fell.

But wait a minute. Those clothes… John stepped forward, his heart beating faster. That grimy, ripped, blood-stained uniform…it couldn't possibly be…could it? John's eyes moved to the man's shoulder, and he saw it: the 'Atlantis' patch. It was stained, and it had frayed so badly that you could only read 'lant', but John knew it was the same patch that he bore on his shoulder at the exact moment. His pulse quickened.

After six long months, they had found Rodney McKay.

"Ford! Teyla!" John shouted, his voice loud and with no regard to the fact that they were invading on enemy territory. He rushed forward, grabbing at the door. He jerked the door, and it moved about a foot with a loud creek. The man – Rodney McKay – looked up slowly. John felt a surge of emotion pass through him. Those blue eyes – bloodshot as they were – those definitely belonged to Rodney. He heard the footsteps as Teyla and Aiden came running. With one last tug, the door slid open, allowing John access.

"Rodney!" he shouted, kneeling to a stop before the other man. Rodney's eyes moved toward John slowly. John couldn't stop the large grin from spreading on his face. Rodney! He was _alive_! After all this time, Rodney McKay was sitting in front of him! Teyla and Ford finally reached the cell. John heard their gasps of joy behind him. Rodney's lips opened and closed a few times, as if attempting to remember how to speak. To a man who hadn't spoken a word in six months, it was a difficult task. John was patient, waiting for Rodney's words, expecting a sour, McKay-like "took you long enough" or a "you've come!" or something to that effect.

But to John's utter horror, the mutilated man before him instead whispered in a hoarse, cracked voice, "Who's Rodney?


	2. two

Elizabeth Weir took a deep breath as she stared anxiously ahead at the Stargate. Her hands were clasped tightly behind her back; her ears finely attuned to the eerie quiet that had settled in the control room. Beside her, Peter Grodin held the same aura of restlessness, his eyes roaming from the 'gate to the laptop that sat in front of him. Both fought against the hope that nipped at their heels, recalling all too clearly the times when John's team had gone out to find Rodney, certain that this would be the time, and had come home empty-handed. But this time…it had been different. Elizabeth exhaled, recalling the day that Sora had stepped through the 'gate back to Atlantis for a briefing on what she'd heard, planted in the Genii facility. There had been a smile on the young woman's face as she jogged to Elizabeth, hardly able to contain her excitement. Sora hadn't known Rodney as well as most people, but she had known him – and more importantly, she had been there for the aftermath of his capture. _"Elizabeth," _Sora had said quickly, giving a brief nod before continuing. _"I think I've found where Rodney was taken."_

And it all led up to today. Elizabeth could only pray that Sora's information was correct. She wasn't quite sure how much of this repetitive heartbreak everyone could take. Several times, she had considered stopping the search, but then thought better of it. The 'gate suddenly sprung to life, and Elizabeth tensed. Peter's fingers flew to the keyboard, his pulse doubling. Elizabeth swallowed tightly as the chevrons began to lock. Memories from her last conversation with Rodney before he disappeared ran though her mind, leaving the same old bitter, guilty, self-hating taste in her mouth as always. He had been looking out for Atlantis, as always. Now, after all of the things that had transpired in the past six months, Elizabeth wished she had heeded his plan. But now was not the time to reminisce.

"Incoming wormhole," Peter said aloud, shattering the fragile silence that had settled in the room. Out of the corner of her eye, Elizabeth saw a few people lurking around, sharing anxious glances with one another.

"Raise the shield," she ordered softly. Peter did so without question. A few seconds later, the wormhole was established. Elizabeth swallowed tightly, tension in the air as they waited for John's identification code. She shut her eyes for a long moment before opening them again, trying to steel herself for whatever was to come. A feeble notion, perhaps, but it gave her the strength to open her eyes again and face the 'gate, her fears hidden deep within her.

"Receiving Major Sheppard's identification code," Peter said a moment later, his hand already reaching over to lower the shield.

"Lower the shield," she ordered, her voice wavering slightly with anticipation. She clenched her hands together tightly, each passing moment without 'gate activity tearing at her. Elizabeth shared a look with Peter, and saw her own emotions displayed in his eyes. Her gaze darted back as Sora appeared, a bloody, beaten woman clinging to her for support. Lieutenant Ford appeared behind her, an equally mangled man's arm around his neck. Finally, Major Sheppard and Teyla appeared together, one man between them, each arm around one of their necks.

Elizabeth nearly flew down the stairs to the 'gate, stopping just feet away from the group. Her eyes swiftly took in the group. "Medical team to the 'gate room," she ordered through the radio quickly. John glanced at Teyla, and with a silent agreement, John walked up to Elizabeth. Teyla slowly lowered the man's body to the ground, knowing he would be unable to stand even with her support.

"We need to talk," John said simply, grasping Elizabeth by the upper arm and steering her away. He stopped when they were a good fifteen feet away. Elizabeth tried to look at John as he spoke, but her eyes traveled to the group anxiously. "Elizabeth," John said firmly, and something in his voice alerted her. She snapped her gaze back to him. Something was wrong. She felt it, and she saw it in his eyes. If they had found Rodney, there should have been joy in his eyes. But this? His face was blank, his expression emotionless. "Listen to me," he ordered as Carson and the medical team rushed toward the aid of the three victims. "That man Teyla and I were carrying…" he stopped briefly. "…it was Rodney." Elizabeth's eyes widened, her expression quite clearly wondering why he didn't tell her sooner. She went to go to Rodney, but John grabbed her arm again, stopping her. He walked forward and stepped in front of her.

"We found him," Elizabeth whispered, and John felt his heart plummet at the raw emotion in her voice; the light in her eyes relit. She went to move around him, but he stopped her again. "John…?" Elizabeth prompted.

"He doesn't remember anything," John said bluntly, and saw a million emotions pass across Elizabeth's face.

"What?" her eyes were latched on to Rodney's form. She felt bile rising in her throat at his physical state, as well as a surge of anger directed toward whoever did this to him. Elizabeth's eyes ran over the length of his body, able to see small similarities. It really was Rodney. Tears pricked at her eyes, and she couldn't stop them from falling. Six long months: six long months of pure hell without him, and now he was here, in the same room.

"He doesn't remember who he is, and I'm assuming anything else," John told her. He fell silent afterward, remembering days in the military where prisoners had returned home. They were never the same. John looked at the ground for a long moment, remembering the long beat of panic that had seized his body when Rodney had spoken to him. The panic had long subsided, but it had given away to pain that was even greater in intensity. Elizabeth felt her hands shaking with the news. Rodney didn't remember who he was. Hot, angry tears continued to spill down her face. She was incapable of speaking, so overwhelmed by the situation. John moved forward silently, hugging her tightly. Elizabeth hugged him back nearly as tightly, her hands curling around his black vest, the fabric absorbing her tears. They stayed like that for a long moment, the sounds of the medical team fading.

"Dr. Weir…" a young military man had wandered up, oblivious to what he had just missed. "Ma'am, Sergeant Bates is waiting for you in your office," he was clearly uneasy, not knowing what to make of this. John straightened up, still holding Elizabeth.

"Tell him to reschedule later," John ordered.

"But, sir—"

"Later," John hissed, his voice dropping dangerously, his body stiffening.

"Yes, sir," the young man saluted before jogging away.

John pulled away from Elizabeth gently, his hands on her shoulders. He looked her in the eyes carefully. "We should go to the infirmary," he told her, and she nodded in agreement, a lost look in her eyes. "You gonna be okay?" John asked. He wasn't sure if it was her emotions overwhelming her or if she had gone into shock.

Elizabeth shook her head numbly. "No," she told him honestly, "but I can walk."

* * *

**Author's Note: **Thank you all for your wonderful support and many more thanks to my beta, Hans. I stayed up until five in the morning working things out for this story, and I am dead tired. Anyway, hope you enjoyed and please review!


	3. three

"Carson," Elizabeth stood up quickly as Carson Beckett approached the group. John, Radek, Teyla, Sora and Lieutenant Ford were sitting next to her in a haphazard gathering of plastic chairs. In the far end of the infirmary, Rodney McKay was sleeping, with a privacy curtain drawn around his bed. Carson nodded to Elizabeth and the others in acknowledgement, swallowing in preparation for the news that he had to deliver.

"How is he?" Elizabeth asked softly, her face masked with concern.

"He was beaten pretty badly," Carson started out, swallowing tightly. Elizabeth's eyes fell to the clipboard he was clenching in his hands and she noticed with a pang of guilt that his knuckles were white. She realized then how difficult this must be for him. Sure, he'd treated his friend before, but this was different – _far _different.

"We've cleaned and stitched up what we can; the other wounds will take time to heal," he informed them, his voice somber. "Some of the wounds were infected, but thankfully there wasn't a lot of damage done." Carson bit his lip for a long moment before continuing.

"The left ankle is fractured, and there is extensive damage to the kneecaps. Tomorrow at 0600 we're planning on performing surgery to reconstruct them," Carson added, looking to Elizabeth for approval. She nodded, her expression solemn.

"Right," he murmured, glancing down at the chart though he had already memorized it all. "His body is suffering from nutrient deprivation and dehydration, but those aren't nearly as bad as I thought they would be," he sighed softly. "There's also three broken ribs, two broken fingers, and some head trauma," Carson concluded.

Elizabeth closed her eyes, letting it all sink in before she spoke. "The head trauma…" she began, opening her eyes. Carson could see the raw emotion that dwelled there; the emotion that was usually hidden behind the mask of a leader.

"It wasn't serious," Carson explained, "He was lucky." Realizing what he said, Carson wished he could take it back. _Lucky!_ Rodney had been far from lucky."It didn't cause any damage to the brain, just surface damage. He'll have a hell of a headache the next few days, but that appears to be the extent of the injury."

Elizabeth sighed softly. "So, the head trauma doesn't have anything to do with – "

"No," Carson shook his head. "The chances are very, very slim." His eyes met hers, and her heart sank. Callous as it sounded, she had hoped that the head trauma was the reason for Rodney's amnesia. It was better than the alternative.

John stood up, eyes intense. "So he's gonna be okay?" he prompted Carson.

Carson nodded. "Ay," he affirmed, and what was left unspoken hovered in the air. Rodney would be okay – at least physically. "I gave him some medications for the pain. So he'll be sleeping most of the day," Carson finished before walking away, attending to another patient. Elizabeth glanced sideways quickly. Everyone's gaze had settled on her, waiting for her to say something. She dropped her head briefly, her eyelids falling as well. On one hand, she was relieved that Rodney was going to be okay. On the other hand, she felt terrible that these things had happened to him, and she worried that however fine physically he was going to be, the Genii had left more than just visible scars to remind him of his time in the prison. Elizabeth lifted her head. Now wasn't the appropriate time to consider these thoughts. She straightened her back and stood. As much as she wanted to stay, she had to go. There was work to be done on Atlantis. After her duty as a leader was done, she would be free to continue her duty as a friend.

"We should get back to work," she announced. "He won't be able to talk with us until after the surgery," her words were reasonable, but the urge to sit beside his bed every second of the day until he spoke was not. Elizabeth stood still as Teyla, Sora and Aiden got up and headed out of the door. John slowly stood up behind her, not saying anything. Elizabeth gradually turned to look at him, and saw the hollow, burning feeling that was tearing into her stomach in his eyes.

---

"_Number Sixty-Two…" they sauntered toward his place slouched against the corner of the cell. He couldn't summon up the energy to move or fight back, and it wouldn't matter if he had the energy anyway. His hands were bound by heavy steel chains, red cuts formed by the rubbing of the metal on his skin. Dirt already covered most of his body. The two men smirked as they walked. First and Second – he did not know their names, only their faces. First leaned down, grabbing the chain between his cuffs and hauling him to his feet, only to let go and laugh as Rodney's legs crumpled under him. _

In the infirmary bed, Rodney's face contorted.

_Second came into view, kneeling before Rodney with the same twisted sneer on his face. He raised his right hand, the object in his hand a pillow._

His pulse nearly doubled. Next to him, the nurse looked at his heart rate, concerned.

_Second brought the pillow slowly against Rodney's face, using both hands to press the material down. He could breathe for the first few seconds through the pillow. Suddenly, the air he drew through his mouth became hot. His breaths quickened and he knew the oxygen was running out. Despite knowing he could do nothing, he raised his arms, trying to beat off the other man._

His arms twitched, flailing to the side briefly.

_A pounding ache began in his head, and his attempts at escape continued. His lungs suddenly burned, but the breaths he took only fed the fire. A numb feeling ran down to his legs, and he felt his arms drooping._

Rodney's heart rate increased again, his limbs moving randomly. The nurse turned and pulled the privacy curtain to the side, her voice lighting the air. "Dr. Beckett!"

The sudden burst of activity startled Elizabeth and the others. At the call of the nurse Carson immediately set down his clipboard and ran over to Rodney's bed. Elizabeth, jogged after Carson, without a second glance back at John, stopping when she was in front of the bed, just far enough away that she wouldn't get in the way. Carson gave a hurried order to the nurse, and she scurried off. Rodney was tossing and turning, his pulse rate accelerating quickly.

_Second pushed harder on the pillow, and Rodney's eyes watered. He felt as if he was going to explode. His hands fell to his sides, the pounding in his head increasing. And then the pillow moved away from his face. Rodney gasped for breath, hands grasping his throat. He looked up, and Second's smile loomed before him. Slowly, darkness bled into the scene. _

Gently but firmly, Carson put his hands on Rodney's shoulders and rolled him to his side. The nurse returned, handing a syringe to Carson and quickly helping hold Rodney down. Carson inserted the yellowish liquid into Rodney's IV. As the fluid ran through his veins and he fell unconscious, Rodney's heart rate decelerated back to a normal number. Just a few moments later, he was still again, the sedative coaxing his body into sleep.

"What was that?" Elizabeth questioned, her voice a little more high-pitched than she would have liked. Rodney's body seemed to have already forgotten the panic from a few minutes ago; a peaceful look on Rodney's face. Elizabeth wondered with a pain in her heart what was really lying behind that flimsy façade of serenity. Carson rolled Rodney back over onto his back and checked his heartbeat before replying.

"It's hard to tell."

"It looked like a seizure," John commented, walking up behind Elizabeth.

"It could be," Carson sighed discontentedly, watching Rodney as he spoke.

"What do you mean 'it could be'?" John demanded.

"I need to speak with Dr. Heightmayer. There are things called night terrors that do cause the body to act as if it is having a clonic seizure. It usually happens only in children, but…" he trailed off. "Rodney will be fine. Permission to consult Dr. Height–"

"Granted," Elizabeth replied, interrupting smoothly, and Carson hurried off. She stared at Rodney for a long moment, and then took a step toward the bed.

"Elizabeth," John touched her arm gently and she turned. She looked on the brink of tears, her face torn. "You have to get back to work. Beckett and the staff will take care of him. He'll be fine." He wanted to stay as well, but he knew it was for the best if they went to work. Brooding on this would only cause a mental breakdown that neither of them needed. At the very least they needed to try to distract themselves from this.

"I can't," her voice was hoarse and strangled. The last time she had let him go, left him, turning her back on the 'gate as they stepped through…he hadn't come back. She squeezed her eyes shut; some rational, suppressed part of her mind screaming that she was being ridiculous.

"We have to," John told her. Her shoulders sunk, but when she opened her eyes, they were free of tears. There was a numb strength to her, an ability to force herself onward despite her emotions. Slowly, she walked toward John. He walked beside her, his presence comforting.

Elizabeth clenched her fists. The urge to look back was overwhelming, but she couldn't. She didn't know if she could still leave if she did. Ignoring her will, her head turned, and she caught a glimpse of Rodney. One last look. Something she'd been deprived of before. John touched her shoulder after a moment, and she bowed her head and forced herself to continue, a sick feeling in her stomach. "It'll be okay," he whispered reassuringly.

It might, Elizabeth reasoned. But it would never be the same.

* * *

**Author's Note: **I'm sorry for such a long wait! But anyway, I have the next chapter written for the most part, so there shouldn't be such a long wait. As a prewarning, the length between updates might be very funky from now on. The teachers at my school don't realize we have lives (apparently eight hours a day just isn't enough), so I'm loaded with homework. Anyway, just to warn you. If you want to make updates come faster, just destroy Grand Blanc High School on a weekend. :) Just kidding. Well...sort of. I hope you guys enjoyed this chapter and thanks for the reviews! 


	4. four

She was numb. Numb all over. Elizabeth gripped the balcony railing tightly as she stared out into the dark expanse of the ocean. It felt as if her legs would give out on her at any moment. This day had been a trying one; trying to go about normal business when her mind would not stray from the man lying in the infirmary bed. Still, she had forced herself to finish the day's work, reminding herself that Rodney wasn't going anywhere. However, it did nothing to quench the urge to stay with Rodney for every minute, every second that he was on Atlantis.

Tears pricked at her eyes, the full weight of the day falling down onto her shoulders. Myabe months ago she would've been able to handle something like this, but back then she had Rodney to support her. A stubborn voice in her head reminded her that she had Rodney now, too. Yet this was much different. The moonlight illuminated the tears rolling down her face, and shame was added to the plethora of emotions that ravaged her. Rodney's body had been returned to Atlantis, but was his soul still in there? Would they ever have any semblance of the old Rodney back? Her legs quivered beneath her, and she sat down on the ground, leaning against the white banister.

She had never gotten over this, no matter how hard she had tried. They had searched for months, but turned up nothing. Her best friend, her Rodney, he was missing. If Sheppard had come back with tears in his eyes and a body bag at his side, it would've been more acceptable. She would've gotten over it. But this mindless torment was far beyond what she could handle. Questions kept her up every night. Where was Rodney? Was he even alive? Did he wonder what was taking them so long? When she couldn't cry anymore, when sleep finally overcame her, the nightmares came. Nightmares that invariably consisted of Rodney and a dark incident she'd tried her hardest to erase from her mind.

But those screams…those chilling screams… She looked toward the banister, her vision now blocked by the solid white material. As if it could block these thoughts from her mind. Even now, she could hear them. Hear them clearly; just like the day they'd come over the radio. Static crackling, inhuman shrieks in the background, a frantic remark in an alien language… A soft sob fell from her lips, and she wrapped her arms around her legs. Some people said that crying helped. Kate told her to cry, to let it all out. But it never left. It was always there, always drilling into her stomach. Kate, John, Teyla…they all tried to help. But they couldn't. Only one person could, and he wasn't there anymore.

Her mind brought her back to happier times, times when she remembered how to smile, times when she could look in the mirror and accept the person who looked back at her. In the still silence as she breathed in the ocean air, Elizabeth could picture clearly her quarters, the floor-length mirror turned facing the wall. Shame had become second nature. Every spare second not spent working had been spent thinking about Rodney, thinking about her failure, looking down at her hands and seeing those of a killer. If he had been there it would've been different. She knew that now, and she'd known it then. But there was no other option. That didn't excuse what she'd done.

"I thought you'd be out here." Elizabeth didn't move as footsteps approached; immediately recognizing John's voice. She continued to stare at the banister, hopeless thoughts running through her mind. John slowly sat down beside her and leaned with his back to the banister, staring at the door that led back into Atlantis. The simple companionship soothed Elizabeth, even as some part of her questioned why John was out here with her. Why he'd taken so much of his time to console her over the past months when he could've simply ignored it. She didn't know, and somewhere inside she didn't want to know.

"I don't know what to do," the sound of her own hoarse voice came as a surprise to Elizabeth. "I want to be with him. I just keep thinking…what if he's gone tomorrow? Just like before…" she bit down on her lip to try and stop the tears that her own words had provoked. She had never been much of a crier. Until this happened, at least. "But he's not really here now, is he?" her voice was soft. "He doesn't remember anything. He doesn't…he's not…" she couldn't bring herself to say the words aloud.

"I know," John replied softly. "Those bastards," his eyes flared with the inward promise of vengeance, and Elizabeth looked over at him. She knew he could wrap his mind around this; he knew about the promise of revenge. What was known was comforting in these times. They knew so little after they'd lost a man who knew so much. "They tortured him. They made him like this…" the untold fury raged in his eyes, but the real emotion lay in the sadness behind the fury.

"What are we supposed to do?" Elizabeth inquired quietly.

"The only thing we can do," John replied numbly. "Show him what his life was like. Who he was and what happened. The rest…it's up to him." They sat in silence except for the occasional sniffle, each preoccupied with their own thoughts. It was a nightmare come true.

And there was no waking up.

* * *

"Carson, you have to understand that it's going to be a long, hard road," Kate Heightmayer rested her hands on her desk as she addressed the doctor. "No one can imagine what he's been through. The human psyche isn't meant for these things. When they happen, the brain acts in unusual ways to protect itself. If they were trying to gain information from Rodney… We both know he wouldn't have given them what they wanted."

"And if he could convince himself that he didn't know it, then he couldn't tell them anything even if they broke his will," Carson finished, sighing heavily. "I know. I just…are you sure there's not anything you can do?"

Kate shook her head. "No. There are things out there that people have to figure out and fix on their own. I can only help lead the way. What happens next is up to Rodney. He's going to be going through some trying times when he—"

"We've been through the trying times already!" Carson interrupted. Kate looked up at him, shocked at his outburst. Carson rubbed his face with a hand, sighing. "Aye, I'm sorry. It's just…it was so horrible after he went missing. It was like there was this big…hole in the expedition."

"There was," Kate murmured softly.

"Everything went down the drain after that. We have nothing left." Kate saw the sorrow and the anger in his eyes, and she knew it belonged to nearly every soul on Atlantis. It was hard, trying to help everyone when she could hardly help herself. "And just when things look up…" he trailed off. Kate knew what he was going to say. They were all so excited, so elated, and then came the news about the memory loss. Something that couldn't be fixed with a few injections.

Kate reached forward, touching his hand reassuringly. "We have something, Carson," she told him gently. "We'll always have it."

"Yeah?" Carson sighed. "What is it?"

Kate smiled wearily as she replied. "Hope."

* * *

Radek Zelenka collapsed into one of the chairs by the lab bench and rubbed a hand across his face. It suddenly felt as if his skin contained twice the wrinkles as usual; his age progressed by the unforeseen events of the day. They had finally found Rodney. The relief had nearly brought tears to his eyes. A day hadn't gone by when the expedition hadn't felt his loss. As hated as he appeared to be, Rodney had an effect on people. The science team, which Radek had been temporarily heading in Rodney's absence, was far crabber, no longer viewing their job as a pleasure or the things they got to see as magnificent – the same science team that had, for the most part, disliked Rodney. To those that had seen beneath Rodney's shell of antagonism, apathy and hypochondria, things had been much, much worse.

Elizabeth had been a terrible mess of emotions in the first few weeks. No one had known what to expect – desperation, sadness, anger. It seemed only John Sheppard could figure her out. He had held her, consoled her and watched over her. Radek wondered about this. Was John doing this out of the kindness of his heart, or some subconscious promise he had made to Rodney's memory to protect what Rodney loved most? John hadn't appeared to be making time for himself so he could recover. There had been whispers of a relationship between the two, but the rumors had quickly dwindled, the addicting entertainment of gossiping gone.

Just after Rodney's kidnapping, they'd been thrown into chaos with the Wraith attack on its way. John…Radek had never seen him that way; so fervent in his passion to rid the galaxy of them. It wasn't as if anyone harbored fuzzy feelings for the Wraith, but the way John talked about them during that time… Radek knew he was taking his anger at the Genii out on them. Eventually, the attack had been stopped…but at what price? Elizabeth had been so fragile after Rodney's disappearance, and to have the guilt of what happened during the siege piled on her…it had broken her spirit, just like the Genii had broken Rodney's soul.

Radek himself had been strained beyond words. He'd taken charge of the science department temporarily, trying to deny the thought that it wasn't going to be quite so temporary. The overload of work and emotions terrorized his body. He wasn't sure the last time he had eaten something other than power bars or a quick snack, or, for that matter, had more than a sparse few hours of sleep here and there. Somehow it had seemed so wrong to sleep fitfully while Rodney was out there somewhere. Questions that could not be answered had run through his mind nonstop, making it hard to focus. Everywhere he turned, Rodney's absence was noticeable. He couldn't escape; couldn't think of anything else. If Rodney had been here, things would have been better. They would've come up with another plan to destroy the Wraith, a better one. _Any_ other plan would have been better.

But that was in the past, and this was the present. They all were broken; their spirits torn to pieces and scattered about the tiers of Atlantis, but Rodney was back. That was what they really needed to focus on. By some act of God or sheer coincidence, Rodney was on Atlantis. Things would never be perfect again, but they could get better. It was possible that Rodney could remember again in due time. If there was a chance, then Rodney would remember. Radek would make sure of that.

* * *

**Author's Note: **Not much to say; just I hope you guys liked and please review!


	5. five

**Author's Note: **Yes, Rodney will be back and awake soon. :) Sorry about the length between updates, but I hope you enjoy. Just thought I'd pass along a reminder to clear up a few things: this is a prequel to "Cold" (which you can find in my homepage under ficlets) and does not take into account what occurred during "The Siege". And yes, there will be tons more on what happened during the attack as well as more Sora, Teyla and Aiden. Just give me time. Anyway, have fun reading, and if I don't update soon, happy holidays!

---

It was so hard to focus. Elizabeth stared at the scientists rambling on in front of her, and all she could think about was how Rodney and Radek should be the ones sitting here. She remembered too clearly how they would battle for conversational dominancy to see who could tell her the exciting news first, cutting each other off in the process. But instead Rodney was lying in the infirmary bed, Radek sitting beside him. Radek. She smiled slightly as she thought of him. Always loyal, no matter what. He'd been one of the few to breach the walls she'd so firmly placed around herself after the siege. No lies passed his mouth – he didn't tell her that what she'd done was the right thing to do, that it didn't make her a murderer – but he made it clear that he would always support her, that he would always be there if she needed him. Perhaps he understood more than most, for he shared the guilt that plagued her.

"…if we decrease power usage by point zero six percent, then the power in the ZPM…" she tried to focus. The ZPM… Here they were talking about how to best use it when they shouldn't even have it in their possession. Elizabeth sighed, rubbing her temples with her fingertips. After the trauma of the siege had intensified to something deeper and darker, she'd been able to hide it within herself and go along with routine. But now that they had found Rodney, it had become so much harder. If only he had been there… She'd heard whispers of the same thought plaguing Atlantis while they'd waited for the Wraith to strike, desperately trying to come up with another way. Had Rodney been there, she knew it would have been different. Despite what he'd said the last time they'd ever spoken, arguing heatedly that taking the ZPM was their only option, she knew that eventually he would've come around, would've understood, would've thought of another plan.

The scientists had fallen silent, and she realized they were waiting for her opinion. "I'll think on it," she said finally, dismissing them. The two walked out of her office in silence. She leaned back in her chair, closing her eyes for a brief moment. When she opened them, John was leaning against the doorframe, watching her.

"Rodney's awake," he informed her, and Elizabeth sat up. "Carson is running tests now. He says Rodney will probably fall asleep right after; that you and I should wait until later to come and visit." Elizabeth nodded numbly at his news, waiting for it to sink in.

"So is he really…?" she trailed off, unable to complete the sentence.

"He doesn't remember anything," John answered, stepping away from the doorframe and walking into the office. "All he knows right now is that he was a part of this base before everything that happened."

"Right," Elizabeth said, taking a deep breath and releasing it. Everything was so new, so hard.

John walked over to her, sensing her sorrow and apprehension, and set his hands on her shoulders soothingly. "You have to be strong," he told her softly.

"The strong Elizabeth," she murmured with a sigh. "Yeah…" she turned her eyes away from him. "No one's seen much of her lately."

"Hey," John touched her chin and gently turned it until she was facing him again. "It's going to be okay, I promise."

"You don't know that," Elizabeth replied, her voice hollow. "You don't have any control over what's going to happen."

He couldn't deny it. John watched her fight back tears, and he wished that he did have control over what would happen. Everyone – Elizabeth, Rodney, Zelenka, himself, all of Atlantis – had gone through more than enough. John leaned forward and pressed his lips to her forehead softly, an expression of comfort because he had no hopeful words, no more guidance to give.

"This is where I draw the line," a nasally, whiney voice cut through the air, and John drew back to face the doorway were Doctor Kavanagh stood, an expression of disgust on his face.

"This isn't what it looks like," Elizabeth replied slowly, tired of saying the same thing over and over again to different faces.

"You think you're so smart, trying to cover it up as friendship. _Please. _Everybody knows," Kavanagh continued, walking to Elizabeth's desk and slamming his palms down on the surface.

"Kavanagh…" John said in a low, warning voice, but he was ignored.

"You're supposed to be the good example for everyone," Kavanagh reminded her. "But instead you're fraternizing with a co-worker, not doing your job right…"

"Not doing my job right?" Elizabeth echoed, and stood up so they were face to face. John stood by her side, his eyes moving between the two, ready to intervene.

"Oh please. My idea of power usage for the ZPM was brilliant, but you just blew it off!"

"I said I'd think about it."

"Yeah," he sneered. "Don't make me get started on your recent decisions. You're not fit to be leader of this base, you never were!"

"Kavanagh!" John shouted, anger written in his face. "Shut…the hell…up."

"Not this time," he shook his head in defiance and faced Elizabeth again. "Your decisions have endangered people time after time. After McKay disappeared you sent teams after him for weeks! We could've used those to find power sources and ways to fight the Wraith."

"I'm—" John took a threatening step toward the other man, but Elizabeth stopped him.

"Let me handle this," she told him, and brushed past him. Kavanagh turned to face her, their angry faces just inches apart.

"It's your fault we didn't have any other plan when they came. If you would have done something then all of those people wouldn't have died. We could've gone home by now. The way things are," he made a wild encompassing gesture, "that's your fault."

"I sent those teams to find Rodney because if there was a solution, he would be the one to find it. And I have a heart. Not that _you _would know anything about that, Kavanagh," she retorted, venom in her voice.

"You have a heart?" he questioned. "Sorry, I didn't realize. Do people with such big hearts murder tens and tens of people?"

Her hand moved of its own accord, clenching into a fist, launching forward and meeting its target square on Kavanagh's cheek. A burning pain ignited her hand, but the crude satisfaction she'd gotten was more than worth it. The doctor stumbled back, holding his cheek. John moved quickly, pulling Elizabeth away and standing in front of her. Two marines rushed in, looking from side to side, trying to figure out what had just transpired.

"Get out of here, Kavanagh," John said evenly. Still cradling his cheek, the other man took a couple of slow steps backward, never once breaking eye contact with Elizabeth.

"I hope you know you just proved everything I said to be true," he informed her.

"OUT!" John bellowed. Kavanagh sneered before turning and walking out of the room. "I'll handle this," he told the airmen, and they nodded and left the room. When John turned to face Elizabeth her back was against the wall, her eyes shining with unshed tears. Any angry, criticizing words that had been forming in his mind fell away.

"He's right," her voice was empty. She blinked and the hot tears began to fall. "Everything he said…" she slid down the wall until she was sitting. "…It's true." John knelt down and tried to comfort her, but his words had no effect. She had gone to a dark, deep place; a place where only one man had been capable of reaching her, the same man that didn't even have a hold on himself anymore: Rodney.

---


	6. six

_"Well, we have to power the shield somehow. We're sitting ducks without it!" Doctor Kavanagh's angry voice cut through the tense air of the briefing room._

_"I am well aware of that," Elizabeth responded, rubbing her temples with her fingertips and looking around the table at the others seated with them. "We need a ZPM, I know. So tell me how we can get one."_

_"The 'gate addresses that your other self gave us – the ones we haven't gone to – we haven't been able to establish a connection to," Radek Zelenka chimed in as he removed his glasses and rubbed the bridge of his nose. "It is probable that the planets have shifted, in which case we can account for that and establish a wormhole, but those equations take time."_

_"Time that we don't have," Major Sheppard reminded them all bluntly as he leaned back in his chair._

_"Right. For the sake of argument, say we somehow get a ZPM," Elizabeth said, looking around at them. "'What can we get out of it?"_

_"The shield," Radek replied._

_"That's it?" Elizabeth asked, desperation on her face. "No weapons, no…"_

_"I'm afraid not. The shield it," he gestured, "-it takes a lot of power. If the Wraith…if they keep firing down at us I'm not even sure how long that will last. A week, perhaps."_

_"A week?" Elizabeth sighed heavily, slumping back in her chair._

_Radek sighed. "That's all. If we'd be able to somehow get two ZPMs, then there are more options available. If we put all power to the shield, we could be here for a few months unharmed."_

_"They will not stop their siege," everyone's eyes moved to Teyla. She'd stood up a while ago, leaning against the wall as she listened to the conversation. "The Ancestors lost the same war because the Wraith were greater in numbers. They will never stop coming." _

_"We have to fight back," John said. "We're sitting ducks otherwise. They'll just wait until the shield runs out and then attack. Meanwhile they're sucking the life out of everybody else in this galaxy while we sit behind our shield."_

_"We could use the second ZPM for weapons," Radek conceded. "Now, we don't know how much of the weapon supply is depleted, but if we get a fully functioning ZPM, it'll be easy enough to tell."_

_"So if we manage to acquire two ZPMs, we have a shield for a week and maybe some weapons," Elizabeth clarified._

_"Teyla can communicate with the Wraith," John added, glancing over at her. "We've got to be able to use that somehow."_

"Tell me how," Elizabeth replied. Silence was her answer. "The Wraith are coming," she announced, standing up and clasping her hands behind her back. "We're at war, just like the Ancients were. They lost, but we can't afford to lose," she looked around the table with a small sigh. "Radek, I want you and a small team working on accounting for the planetary shift problem. Fix it so we can get those ZPMs. Send the rest of the scientists into the unexplored parts of the city; have them take Bates' team in case something should go wrong."

_"In case something goes wrong?" Kavanagh interjected. "We're exploring **now**? We don't need any problems that doing just that can cause." _

_"I know. But there's much here we haven't discovered. There could be weapons out there, a key to defeating the Wraith… We have to try."_

_"The Ancients lost. Nothing of theirs is going to help us now."_

_"I'm sorry you feel that way," Elizabeth said, dismissing his thoughts and receiving an angry sigh from the other man. "Lieutenant Ford, Teyla: I want you to go to the planets the Wraith will pass on their way here. Warn them the Wraith are coming. They are welcome here, but make sure they know what could happen. Carson, I want you to give the gene therapy to everyone you possibly can. If they didn't take, try again. John," she looked over to him, "as soon as the gene starts taking, start training pilots." _

_"Doctor Weir," Kavanagh spoke up and all eyes turned to him. "I know none of you are going to like this suggestion, but if all else fails, we know planets with ZPMs. The one with the children, the one where Doctor McKay –" _

_"Nothing has failed yet," Elizabeth interrupted, her voice steely. She gave one final glance around the table. "Let's get to work."_

_---_

The moment Carson Beckett stepped out of his office, his eyes moved to Rodney's bed. A small smile tugged at his lips when he saw Sora there, sitting vigilantly on the chair beside the bed. Carson walked over to them, stopping just beside Sora's chair, his eyes on the young, petite woman.

"He's been in and out," Sora supplied, finally breaking her eyes away from Rodney and looking down at the floor instead.

"Ay, he'll be doing that for a while," Carson informed her. He paused briefly before speaking again. "How long have you been sitting here?"

"I…" Sora ran a hand through her red curls. "I don't know." She sighed and met Carson's eyes, distress easy to read on her face. "To tell you the truth I don't know why I'm here. I hardly knew him. You guys let me free so long after he'd gone. I know his name, and I know what his being gone has done to everyone," her eyebrows drew together and she frowned. "So I'm sitting here, waiting for him to wake up…and I actually care. I…I care if he lives, I care if he remembers or not…and I have no idea why."

Carson smiled slightly as he looked at her. "I suspect it's a part of Rodney's charm," he told her, moving his gaze to the sleeping man. "Everyone hated him, but we all loved him more."

There was a long silence before Sora spoke again. "If I had been able to foresee this in my future…" she laughed hollowly. "Let's just say I wouldn't have believed it. I was so full of hate and…anger." She frowned, her eyes returning to Rodney.

"But you're not anymore," Carson reminded her. "You're better now."

"Better?" she echoed with a harsh laugh. "This is better? Hurting like this?"

Carson sighed. He didn't have an answer to that. "He's going to be okay," he told her instead.

"Physically," Sora spat. "The Genii – my people – they did this to him. They took him and deconstructed him, took away his identity. And he's just one of hundreds. Hundreds of innocent people who will never have the same life again," she looked away from Carson, lest he see the weakness in her eyes.

"Sora," he said gently, "You're not a Genii anymore. The only reason Rodney and the other two are here now, safe, is because of you. You saved their lives."

"Saved them from what?" Sora questioned harshly. "When Rodney wakes up, he won't know anything. Even if he starts to remember, what will we tell him? He'll remember a home. A place of happiness and hope," she turned her head and met Carson's eyes. "He'll remember a paradise and he'll receive the opposite. Tell me, Doctor. How will we tell him that Atlantis, the city of the Ancestors, is dead? There's no hope, there's no happiness, there's no humanity. We're not any better than the Genii, Carson. What we've done is unforgivable." She stood up, blinking furiously to keep her tears at bay.

"Sora," Carson said, trying to get her to calm down. "We're not. We—"

"We what?" she paused, the anger and frustration in her whisked away, leaving her vulnerable and torn. "Atlantis was strong. People here didn't dare hurt others to protect themselves. They were upright and moral and brave. So what are we now?"

"We made a huge mistake," Carson admitted. He opened his mouth to continue, but Sora cut him off.

"That mistake destroyed everything. What we stood for disappeared in that moment, and now we're the disappeared. We sit here and make no amends. We survive day to day. We don't go on missions, we don't try and save people, we don't…" she stopped and shook her head. "We're nothing now, Carson. That's what Rodney's waking up to. That's what I saved him for. Instead of dying in the hands of the Genii, believing in Atlantis and his people until his mind couldn't handle it any longer, I brought him back. I brought him home to see how his people slowly destroyed everything they held dear. He's alive to see everything he wished he would never see. Look at me and tell me I'm making amends now," her voice shook as she spoke. "Tell me I saved him, that everything is going to be okay." Silence stretched between them, Carson unable to find the appropriate words to console her. "Because none of it is true. Every one of us has changed, and we can't go back to how we were." As soon as the words left her mouth, Sora walked away quickly, brushing past Carson and heading for the door.

"Sora!" Carson took a step after her. "You have to trust that things will get _better_!" he continued, but Sora didn't appear to acknowledge his words, walking out of the infirmary without so much as a second glimpse backward. Carson sighed heavily as he sat in the chair Sora had previously occupied, looking down at Rodney. Slowly he reached forward, placing his hand on top of Rodney's. "I hope you get well soon, lad," he whispered softly, "We need a change around here."

---

**Author's Note: **Okay, so I said Rodney would be awake this chapter...and that was the plan! Just turned out different. He'll be in the next chapter. :) Anyhow, I hope you guys enjoyed.Sorry if it's not as good as normal; written while procrastinating midterms and finals. Tomorrow are my last two - health and honors English- and then a three day weekend! Which means hopefully a quick update here. Thanks to fififolle for the beta! Oh, and to all people who support het pairings besides Shep/Weir, the Isis Awards nominating period ends on Friday. Anyway, sorry for the rambling and I hope you enjoyed!


	7. seven

She'd never seen him like this. He'd been in the infirmary hundreds of times, but it was different now. His eyes darted around the room, quick movements to keep him above the sea of his own fear, as if he could make sense of everything by observing. Just like always, he took in more than anyone else would normally see; focusing on telling little pieces and trying to fit them into a puzzle for which he didn't have all the pieces. Fingers, always in motion, tapped against the railings of his bed. It comforted her to see that the natural quirks remained. If they did, what else lurked beyond the damage dealt to him?

Still, he was different, even in silence. Perhaps they'd never get the Rodney they knew back, but she had begun to discover he was her only hope; Atlantis's only hope. Nothing and no one could right their wrongs, but they were in a rut. A shallow, dark and hopeless rut in which they tortured themselves everyday. Maybe it was their punishment, maybe it was just; but they couldn't live like this. They'd proven it was possible to survive, but not a single one of them had lived since the siege. So their punishment was to survive beneath the weight of their actions, but they were born to live. They deserved to be punished, but it was too much to bear. Either someone had to come and lift the weight of their sentence or they would be crushed beneath it. Rodney was the only man they knew unaffected by what they had done; he was the only man able to help them deal with it, to help her.

Something had happened when she hit Kavanagh; a catalyst letting forth a realization. Elizabeth had been at some low points in her life, but this was her lowest; the lowest she would ever be. Was this what she was born to do, put a mask of apathy on during the day that gained more and more cracks as time passed, do her job, and then retreat at night and let the mask fall off, let the tears drown her? It seemed years ago, but it was only less than a year ago she, and everyone here, had had a purpose. They didn't deserve life anymore after the lives they'd taken to preserve it for themselves, but they'd been granted with it. Their own lives weren't just their lives anymore. Everyone that had died during the siege, everyone that had died during the expedition, would have died for nothing if the people of Atlantis continued to simply survive. They had to do something to prove that those people hadn't died for nothing.

They had to make amends. Elizabeth knew it wasn't going to be easy and she knew this clarity would not last long. She had more demons to face than most, but it was something she had to do: for herself, for the expedition, for all those that had died, and for Rodney. Things were broken and they needed to be fixed. A long road lay ahead of them, but only if everyone chose to take it.

Their path started now with Rodney. Frozen as she was to this spot, she needed to leave Carson's office, get her limbs to take her to Rodney's side. Maybe he would remember and maybe he wouldn't. Either way, she had a feeling that he would have to relearn things. When he did, he would know things were different. It was then they would have to tell him everything that had happened; what they had done. This was their path to redemption, to salvation: they had to admit their guilt and to try and make amends. She only felt so horrible when she knew that Rodney, who had gone through so much, would have to go through something that may prove as worse as his torture: his recovery.

But she prayed that one day, things would be okay. Nothing would be perfect ever again, but she was more than willing to settle for it being better than this hell they were trapped in. Rodney and everyone else, including her, would be back to normal, as normal as they could be. What each of them had been through would stay forever, but guilt and suffering are particular things. When they are not faced, they build and become nearly insurmountable. No one on Atlantis had faced theirs, hiding from it instead, sobbing and mourning and wishing things had gone differently. It had been several long months, and that period had to be over. The people of Atlantis had to face their emotions, face what they had done and defeat its crippling, lasting mark on them, use it to help them help others again. It had to be this way. She was afraid of what would happen when Rodney started asking questions, but she was even more afraid of what would've happen if he had never returned and the questions went unasked.

- - -

_"Doctor Weir!" Teyla's voice slowed the other woman's hurried pace enough so the Athosian could catch up to her. "The last refugees have been assigned living quarters, as well as my people."_

_"Good," Elizabeth replied with a sigh, resuming her pace and making a note on the data pad she carried. "How many?"_

_"Many," Teyla answered, "But I'm afraid it is only a scarce few compared to those who still remain on their home planets. They were unwilling to leave."_

_"We did the best we could," Elizabeth said, and paused for a moment as if she was debating the truth of her statement. "Radek just called me down to the lab. He says he might have something on the location of one of the ZPMs. You're welcome to join me."_

_Teyla nodded, "Very well." They walked in silence for a moment before she spoke again, tentatively this time. "Doctor Weir, we are fighting a war. We will need all of our warriors. None can be spared."_

_"I know," Elizabeth answered, and averted her eyes. "I already called back the teams searching for Rodney." _

_After that, no words passed between them._

- - -

Elizabeth didn't know what to say to the man lying in the hospital bed just feet from her, the man whose confused, muddled eyes slowly focused on her, asking all sorts of questions without speaking a word. Carson stood beside her for just a moment, squeezing her hand in support before turning and attending to his many duties. Elizabeth swallowed tightly and sat down in the chair beside his bed, attempting a friendly smile.

"My name is Doctor Elizabeth Weir," she said, somehow finding her voice in the muddled mess of her thoughts and emotions. "You are on Atlantis now, you're safe." It felt as if this wasn't her Rodney; she was talking to someone else.

"Elizabeth," he said, his throat hoarse as he tested the name on his lips, weighing it. She pressed the fake smile forth again because he had no idea that hearing him say her name after all this time sent tears building behind her eyes. "Where was I? I remember…" he frowned, his eyebrows drawing together. "I remember being tortured. I…I don't remember anything besides that."

"We know," she replied softly. "You were a part of this expedition, the chief scientist. On a mission about six months ago, you were kidnapped by an enemy called the Genii. That's where you've been all this time. We searched for you, but we never found you until now."

He took a moment, absorbing the information. She had no idea how this must feel to him, how frightening it must be to know nothing but torture. "What…what was my name?"

"Rodney McKay," Elizabeth answered, "Your name is Rodney McKay."

"Rodney McKay," he repeated, and sighed softly. "I don't remember anything about myself, about this place, about my life. All I remember is that cell." An odd look took over his eyes, and Elizabeth struggled to hold everything in. She knew that closed expression; she had seen it too well when she'd tried to talk to him about what happened between him and Kolya. "Will I…" he paused. "Will I ever remember?"

"We don't know," Elizabeth replied softly. "I hope so. The resident psychologist here believes that the Genii must have tried to extract information from you. In order to keep that information a secret, she thinks you made yourself believe that you didn't know it so much so that over time you really didn't," Elizabeth sighed, looking down at her hands before looking back up at him. "Actually, she explained it better. But…we're hoping that somewhere in there you remember. It will just take time." Elizabeth stood up slowly. She wanted to spend every second by Rodney's bedside, to stay with him and never leave again, but every second she did spend with him sent her emotions into a deeper and deeper mess. "Until then, once you heal we'll show you your quarters and you're free to do as you like. I'm sure you have a lot of questions, but Doctor Beckett says you need your rest."

Rodney nodded distractedly at her words and Elizabeth slowly turned, walking toward the exit of the infirmary, feeling numb. When she reached the doorway, she turned to glance back at Rodney. His eyes were looking over everyone again, trying to put that puzzle together in his mind. She'd known he didn't have all the pieces earlier, but now she realized he didn't even have a pattern; he didn't have the slightest clue where each piece went. Her eyes moved to his hand, and she saw his fingers tapping against the bar again.

Rodney wasn't past hope. None of them were.

- - -

**Author's Note: **I thought we all deserved a happy chapter :) And see? Rodney is finally awake! Look for some conversation between John and Liz next chapter, as well as some thoughts from Rodney. (Of course, the chapters seem to write themselves, so no guarantees here lol) Thanks to fifi again for the beta! Just wanted to remind you guys again that this is a sequel to "Cold" and occurs after S1 up to "The Gift" and an AU of "The Siege" (which you will come to hear about sometime soon). Also, this is rated _mature_ - there will be flashbacks to Rodney's time being tortured that include extreme violence and nonconsensual sex. Probably won't be there for a while, but I don't want to surprise anyone there. Anyway, hope you enjoyed!


	8. eight

**Author's Note: **Okay, I know you must be getting sick of this, but in addition to "The Siege" and all episodes from that point, we're also going to **disregard the events of "Hot Zone." **They did not come across the virus and Dumais and the others did not die from it. This has a point in the plot, I swear it :) Also...It's been forever and a day since I last updated this, and I apologize. So, to make up for my guilt, I've made this chapter extra-long. :) Hope you enjoy!

- - -

Kate Heightmeyer gave a small, peaceful smile to the man sitting in the chair opposite her. His hands were clasped tightly in his lap and on the odd occurrence that his flitting eyes fell on hers, they only stayed for a moment. "I know you must be…overwhelmed," she spoke soothingly, leaning forward with her elbows on her thighs. "But in time, I think you'll begin to think of Atlantis as your home."

"You mean I'll eventually _remember _Atlantis as my home," Rodney murmured softly, his blue eyes finally meeting hers for longer than an instant. "That is what you mean, isn't it?"

Kate paused carefully. "Tell me what you mean when you say that."

He sighed, leaning back in the chair, silent for a long moment. "I've been here for a week. I don't remember anything; don't even get that funny déjà vu feeling. Actually, I can't even remember getting that feeling at any point in my life. But the weird part is I know. I know what déjà vu is, I know my times tables, I know what objects are called, I know how to speak correctly… The thing is that I don't remember anything that means anything. I don't remember anyone's name, anyone's face, anything about my life before that cell…"

"But you remember the little things," Kate stated softly.

"A lot of good they do," Rodney said scornfully. "My friends, the people I apparently referred to as my surrogate family, they had to introduce themselves to me." He looked away, his gaze skittering along the carpet.

"You're scared that you'll never remember, aren't you?" she questioned, tilting her head, waiting for him to continue onward.

"I…" he rubbed his temples with his fingers, his hand covering his face. "God, yes. It seems like…they're all expecting me to remember. Waiting with baited breath. And I don't know if I'm going to. I _want _to remember and everyone else wants me to remember, but… Nothing has come to me yet. I just…"

"If you don't get your memories back, there's still a future for you here," Kate told him gently. "Regardless of whether or not you remember, you're still family and we all still care about you."

"What would I do?" he looked at her, any shields he had now fallen. He was just a man, a man once broken in the shadows that had seen the ray of hope but now wavered to step into the glowing light.

"You'd make your own memories," she told him, smiling tenderly.

"Right. I should've thought of that," he replied, a small smile on his face, the first true smile Kate had seen since his arrival. After a brief moment, he spoke again, tentatively. "I…"

Kate raised her eyebrows, encouraging him forward. "Whatever it is, you can say it," she informed him.

"I'm just wondering… Doctor Weir, she came and stopped by my room once I was released from the infirmary. Just the once. She… She told me that I, John, Teyla, Aiden and myself were very close."

"You all were very, very close," Kate confirmed, nodding her head.

"I just…" he sighed, shifting in his seat. "John, Aiden, and Teyla have all been keeping their tabs on me. Stopping by for visits, watching me or following me when they think I don't know they're there… So why haven't I seen Doctor Weir? Why has she only stopped by once after the doctor released me?"

Kate frowned. "This is…difficult for me to explain to you. It isn't that Doctor Weir does not care for you. You two were extremely close before you were captured; perhaps the two closest people in Atlantis. She was devastated when you left. But you're back now, back without your memories, and she needs some time to adjust."

Rodney smiled tightly. "She's not the only one."

- - -

"_Elizabeth!"_

_Elizabeth turned at her name to see Peter Grodin running up to her, data pad in hand. "Peter," she greeted with a tight smile. "I hope you're here with good news."_

"_I'm sorry, but it's just the opposite," he apologized. Elizabeth stopped, turning to face him. "Major Sheppard and his team have returned from one of the potential ZPM addresses Doctor Zelenka gave them – just some cave men, not even a myth about the Ancients. They searched the nearby area but a blizzard was blowing so they couldn't go far. Either the ZPM was somewhere else on that planet or removed a long time ago, or Doctor Zelenka was incorr—"_

"_Let's just stick with the first option," Elizabeth interrupted._

"_Right," he replied. "But that's not the worst of it. As you know, the science team split up to search the city more effectively. Dumais, Wagner, Simpson and Peterson were infected with a virus from what appears to be an Ancient lab. Doctor Beckett got the call and went with a medical team in Hazmat suits."_

"_How are they?"_

_Peter looked down, refusing to meet her eyes. Elizabeth felt her heart rate quicken. "Carson and his team are awaiting orders to return to the city."_

"_I mean Dumais and the others," Elizabeth told him, frowning._

"_They…" he looked up, and for the first time since their impromptu meeting, Elizabeth noticed the bags beneath his eyes, the reddish tinge to them… "They all suffered from an acute brain aneurysm," he said softly._

"_They're dead," the words fell from her mouth hollowly. "You mean they're dead." Tears stung at her eyes and she shut them tightly. "The Hive Ships aren't even here yet and people are dying by my order," she murmured softly._

"_It's the right thing to do," Peter assured her gently. "We need to find some defense against the Wraith or all of us will die."_

_Elizabeth nodded numbly, but all that kept repeating in her mind was: four down. How many more left to go?_

- - -

"John, I can't," Elizabeth replied earnestly. "I…It's just…" she turned her head, her eyes falling on the water just beyond the railing of the balcony they were standing on. "I just can't."

"You can," John told her encouragingly. He sighed softly when she didn't reply. "You know you have to."

"Why?" Elizabeth questioned, her eyes snapping to his. "Why do I have to? You…" she stopped, knowing her frustration was born from other emotions, knowing that she had no right to say the words on the tip of her tongue.

"I what?" John prompted, his intense stare shooting through her.

Elizabeth couldn't meet his eyes. "You don't understand," she completed quietly. "You don't understand what it feels like when I look at him."

"Yes, Elizabeth, I do," John replied, gritting his teeth. "I understand because I feel it too. Rodney was my best friend."

"Aren't you going to say that he _is _your best friend?" Elizabeth incited hollowly.

"I understand because every time I look at him I see our Rodney McKay," John continued, ignoring her comment. "And it hurts. It hurts like hell seeing him walk around Atlantis knowing that he's not the same man we knew. I hope to God that Rodney's memories are in his head somewhere, because surprisingly enough there's nothing else I'd like to hear more than his smart-ass remarks."

"Everybody keeps saying that," she informed him. "That Rodney is in there somewhere. But what if he isn't?"

John looked at her for a long moment, forming his words carefully. "Rodney told me something once; something you'd said to him. You told him that you wished you could give him a new childhood. To replace all those memories of what his parents said to him with happy ones. Maybe he's finally getting that."

"He's never going to have a happy childhood. All he is now is – "

"A blank slate," John interrupted. "He can't go back in time, but now he's got the chance to start over again. Isn't that what you wanted?"

"He has a new life now," Elizabeth said vacantly. "No memories. A new life…without me."

"If you just stand out here and brood, you're completely right!" John hissed, frustrated. He sighed, running a hand through his hair. "Elizabeth… I'm asking you to go talk with him. Help him get his memories back. If he can't…then help him start over. He may not have his memories, but he's still Rodney."

"Memories are what make us," she replied softly, turning toward the railing, sighing. "I'm sorry, John. You're right. I should go talk to him. It just…hurts. All this time I've thought of things to say to him, to show him… But now I don't know what to do."

John moved to stand next to her, placing his hands on the railing. "You were optimistic about this the other day. You said it would be okay no matter what. You had hope," he paused, and they looked to one another. "What happened?" he asked her gently.

"I thought too much," she whispered, gazing up at him. "Rodney being back…it's a second chance. A blessed second chance to all of us."

"You don't think you deserve it," John murmured, suddenly realizing what had brought about this sudden change in her thoughts.

"Do I?" Elizabeth responded, turning back to face the water. "I had a nightmare last night. The same one I always have. Their screams over the radio…the Wraith in the city…" she sighed. "I'm not so sure all of those people would wish me a second chance, would wish that Rodney came back for me."

"It wasn't your fault," John told her firmly. They'd had this conversation many times, and it always ended the same. He strived to have her understand that her actions were justified, but she never let it sink in, never thought for a moment that he might be right. "It was the _Prometheus _or Atlantis. I'm alive today because of you."

"And they're all dead because of me!" Elizabeth replied, fighting the tears building in her eyes. "I expected tough decisions when I got here, but not that! Not—" she turned away. "I don't deserve a second chance."

"A second chance to have a happy life," John finished. "Look, Elizabeth," he grasped her arms gently, turning her to face him. "Whether you think you deserve that or not…he's back. Rodney is here, alive and well. It's about taking the opportunities you're given, not whether you deserve the opportunities." He let his words sink in. "Just talk to him. For me," he finished, looking her in the eyes.

"I…" her eyelids fell shut for just an instant before she opened them again. "All right," she relented. "I'll go talk to him.

John smiled slightly. "Thank you," he whispered. The brief silence that had settled over them was broken by the sound of an Ancient door being opened. John and Elizabeth both turned to see who had stepped out onto the balcony with them.

"Rodney," Elizabeth breathed softly, her arms tensing. John glanced at her with concern for a brief moment before moving his eyes back to Rodney.

"Hi," he said slowly, pushing his hands into his pockets. "I…I, uh, hope I'm not interrupting anything," he mumbled, his eyes averted.

"No," Elizabeth told him, tilting her head. She took a tentative step in his direction. "You're fine. Was there something you needed?"

"Actually, I…" he looked up. "I was hoping I could talk with you, Doctor Weir."

Elizabeth was silent for a long minute, her mind digesting his words. "Yeah," she replied. "That's…fine. I—" she turned to John.

"I was just on my way to my quarters anyway," John excused, walking toward the door, a small hint of a smile gracing his tired face. "I'll see you two in the morning," he told them, clapping Rodney on the shoulder as he passed.

"So," Elizabeth said as the door closed behind John. "What did you want to talk about?"

"Me, actually," Rodney replied, walking up to the railing, standing next to her. "I want to know what I was like before the Genii…before I forgot. People around here have told me you're probably the best person to ask."

"Oh," she mumbled, turning her head so he could not see her face. Tears had begun to sting at her eyes. This was the one thing she did not wish to speak of.

"Look, Doctor, I know this must be hard for you, but…I need to know," he said softly, frowning.

"Elizabeth," she said, glancing at him. "Call me Elizabeth." Rodney nodded in reply, a faint smile on his face. "Rodney McKay…where do I start?" she laughed softly. It took her a moment to gather her thoughts, and when she began speaking, she did so slowly, pausing between each sentence, weighing it in her mind, drawing an image of Rodney with her words. "He was an astrophysicist; the best. Always managed to pull some ridiculous plan out of the air to save us all. He liked to pretend that he didn't care about people; like they were simply below him and inconvenienced him. But the thing was, he did care," she said wistfully. "He cared more than anyone really realized. Always trying to save everybody, pushing his team to do their best… He was the greatest smart-ass in this city but when you needed him, he was there. He had issues trusting people, but once he trusted you there was hardly anything you could do to break that trust, that friendship," she faltered, her vision blurred by the rising tears. The words burned her throat as they traveled to her mouth, stung her tongue as she spoke them. "He was my best friend, and I…I loved him," she blinked and felt a tear roll down her cheek. "And now he's gone…" She bowed her head and closed her eyes.

Rodney watched her grief silently, at a loss as to what he should do. Carefully, he placed his hand on her shoulder, waiting for her reaction. Elizabeth opened her eyes and glanced to him. Her lips upturned slightly in thanks, and the partial grin was infectious. She wiped the tears from her face, trying to push away the anguish their conversation had intensified.

"There's another reason I came out here," Rodney said slowly, unsure of whether he should tell her. "Maybe your friend isn't as lost as you thought he was," he told her.

Elizabeth gazed at him warily, her mind beating away the hope that pressed itself upon her. "What do you mean?" she questioned.

"I keep remembering something, an object. A necklace, to be more precise. It…meant a lot to me," he told her, his brow furrowing. "I wore it in the cell. It kept me…sane. There was safety in it. Maybe I'm going crazy, but…" he sighed, "The rest of it, it tickles the back of my mind. I feel like I should know more about it, but all I can see is that image and it brings this feeling of…of…" he hesitated before finishing, "…hope. And, weirdly enough… When I think of it, it reminds me of you."

"Oh my God," Elizabeth whispered, staring at him.

Rodney's eyes flashed quickly to hers. "What is it?" he questioned.

Tears were again filling her eyes, but for a different reason than grief this time. He remembered. Not everything, not close, but it was something. And it was amazing what that little detail brought her. Something had been returned to her, something lost: hope. Not just a flickering, dim light, but a solid blaze, something that would not extinguish in time.

"The necklace," Elizabeth responded. "I gave it to you after the Genii invaded Atlantis. We managed to retake the city, but…you almost died. We almost died. I gave it to you because I wanted you to know how important you were to us…to me."

"And I remembered it," Rodney replied in an awe-filled whisper, happiness sparkling in his eyes. "You know what this means?" he questioned, grinning. "It could all be there. All those memories…there could actually be a chance that I might remember them!"

"That's so great!" Elizabeth exclaimed happily, a smile claiming her face. Their celebration was, however, cut short by a flash of purple lightning, followed by a deafening clap of thunder.

Rodney glanced at the black clouds rolling steadily towards them and the pouring rain in the distance. "Maybe we should go inside," he suggested. "I may not remember much, but I do know that pneumonia isn't that fun."

"You're right," she said, nodding, but couldn't hide the small disappointment growing in her stomach as he walked toward the door leading back into Atlantis.

"Hey," he said suddenly, turning. "I know it's late and all, but… Do you want to grab a bite to eat? I understand if you – "

Elizabeth smiled as she replied, "I'd love to."


	9. nine

- - -

"_The Wraith will be here in ten hours." John looked down at Elizabeth, his face impassive. She was sitting at her desk, running her fingers over the cool metal, lost in thought, her face grim._

"_We have nothing," Elizabeth said softly, and moved her eyes to meet his. It was dark, and she could only see the dark edges of his silhouette. She'd given orders to limit power expenditure a week ago. It probably wouldn't amount to much, but she'd had to do something. "Radek's planet was a bust. None of the scientists have found anything useful in the database or within the city."_

"_We're sitting ducks like this," John told her. "When the Wraith show up, we'll only be able to hold the shield for ten minutes. We won't be able to mount any sort of defense. We'll have no choice but to self-destruct the city."_

"_I know," Elizabeth murmured, pressing her palms onto her desk. "We have three possible evacuation sites down. If we get to that point–"_

"_We're not safe anywhere we go. Remember what Teyla told us? We're the strongest hope of survival in this galaxy. If Atlantis falls, it's only a matter of time before everyone else dies, too. There are too many Wraith and too little humans, and if we can't stop them, they'll kill everyone. We need to stop them – at any cost."_

_There was a long silence before Elizabeth spoke. "I'm glad you believe that, John," she said softly, hollowly. "I've been speaking to the scientists. The bottom line is that we need ZPMs and we know where two of them are housed." She said the words slowly, and the implication of what she was saying hit John quickly._

"_You want to take them."_

_Elizabeth stood up abruptly and turned away from him, staring at the 'gate through the glass wall. "I don't want to take them. No one wants to. But we have to, don't we?"_

_John was quiet. She was right. They had no other options. "Yes, we do."_

"_I want you to assemble two extraction teams. I want those ZPMs without any bloodshed."_

"_What about the people left behind?" John questioned, trying to conceal his anger at the situation. "The first planet, they're all just kids! Kids who, before now, haven't lived past twenty-five!"_

"_Tell them what we're doing; tell them we have to take their shield from them so we can destroy the Wraith and save this galaxy," Elizabeth told him. "Bring them back to Atlantis."_

"_And the second planet?" John questioned. He blocked out the memory of his first visit to that planet – the planet that had worshipped the ZPM as an Ancient artifact, the planet where Rodney had disappeared._

"_Don't tell them," Elizabeth said without hesitation._

_He sensed vindication in her words, and said carefully, "We don't know if it was those people that took him, Elizabeth."  
_

"_That's not the point," she replied. "If we told them, they wouldn't let us. Go on, get the ZPM, and get out."_

"_Very well."_

- - -

Rodney McKay stared up at the ceiling of his quarters from his spot on the bed, slowly digesting everything that he had learned in the past week. It had been overwhelming. At times he felt like all of the information was suffocating him, even as the need to know more drove him further. Everyone told him about Rodney McKay, but it was as if they were telling him about another man, not who he used to be. There were good things and bad things, but either way, he couldn't see how he could become Rodney McKay. It was so obvious that these people needed and hoped for Rodney McKay back, but he didn't know if he could give them that.

It was just two days ago that Radek – who he'd come to think of as his tour guide through this whole thing – had said something that made the most sense in the world; that had taken some of the weight off his shoulders. _"It doesn't matter whether you eventually remember this or not; whether you become the old Rodney or not," _he'd said, _"but stop thinking of things like you 'should.' Think for yourself, make friends for yourself, and the rest will come."_

And that's what Rodney had been doing. He found similarities and contrasts in the way he felt about things and the way that the former Rodney had felt about things. But it didn't matter, he told himself. Yesterday, Radek had set him before a computer and left him. Rodney had found an unexplainable sense in the odd symbols as well as the series of numbers, and it had felt only natural to put his fingers on the keys of the laptop and work out the relationships between them that were running through his mind like wildfire. It was then that he realized that, despite how different he may be, there was still a part of him that consisted of the old Rodney. That comforted him, and he'd begun to settle into a small routine. Maybe he wouldn't get his old memories back, but as Kate had said, he would make new ones.

In the mornings, he ate breakfast with John, Teyla, and Aiden. The conversations were stilted and strained at times, but for the most part that awkwardness had begun to melt away. Sometimes Rodney felt like an outsider – when they would talk about old times, or when someone would mention something that happened in his absence, and they all fell silent. There was an odd feeling in his chest that something horrible had happened to these people in his absence, and a driving curiosity pushed him to ask what it was. Still, he pushed it away with the greater feeling that it was not yet the time to ask such things.

He was embracing the small projects that Radek gave him, so much that the other man had stopped being cautious of how work might overwhelm him. When they hit a block or an idle point, the two would go to the mess and grab a bite to eat. Later that day, Rodney would find Elizabeth and they would have dinner together. It was strange feeling, being with her – part of him enjoyed her companionship, and another part of him ached with relief that he'd found her, as if he remembered wishing to see her for months. Since the necklace revelation, he hadn't remembered much.

At least, not much that mattered. In the dark of the night, nightmares continued to plague him. As horrifying as they were, at least they gave him understanding. He knew now that the circular scar beneath the left side of his jaw was caused by a lighter held beneath it for a long period of time. He knew that his pinky bent in an odd manner because it'd been stepped on and twisted and never put right after that. He knew that the panic that built in his stomach when he looked out to the water that surrounded this city was because his torturers had held his head in a bucket of water until he was on the verge of death.

And lastly, he knew why he was sitting here, overwhelmed, a tiny piece of paper that read his identification code clutched in his palm. He knew they'd asked for it at length, that he'd denied them every time and had proceeded to block the number from his mind. He knew that it was because he refused to give up this little number, to doom these people he passed time with now, that he had endured all of that torture.

He had wondered if this act of resistance was his or Rodney McKay's, but now he knew. It was both – they were one and the same.

- - -


	10. ten

"_I want you to withdraw all teams searching the city," Elizabeth set her portable data pad down on her desk and faced Radek. His expression was slightly confused, and she sighed softly. "I've ordered John to retrieve two ZPMs. You'll have them in a few hours if all goes well. Plan accordingly." She turned back toward her desk, hoping that Radek would leave it at that. But really, she knew better._

"What?" He stepped forward, eyebrows furrowing. "Two ZPMs? Where is he – " realization dawned on his face, and the repulsion that followed it nearly broke Elizabeth's heart. "We're going to steal them."

"_We're borrowing them," she interrupted, as if the term made some sort of difference._

"_No," he shook his head. "No, we're stealing them."_

"_They refused to help us when Rodney disappeared!" Elizabeth replied. "They're using the ZPM as an artifact. Why shouldn't we take it? It could save hundreds of people!"_

"_And the children?"_

_She closed her mouth tightly, looking away from him._

"_We cannot steal their ZPM, Elizabeth!" he gestured angrily with his hands. "They won't have a shield without it!"_

"_The best chance of survival is if we take their ZPM," she replied hollowly._

"_You mean the best chance of our survival," his eyes were cold. Elizabeth closed her eyes tightly._

"_We aren't going to go about this in the dark. Our team will tell their leader and invite them to stay on Atlantis during the duration of the siege. Once it's over, we'll give them back their ZPM."_

"_Their depleted ZPM."_

"_Then they can stay here!" she exclaimed._

"_This is not right!" Radek slammed his palm down on the desk and Elizabeth jumped, her face pale. A tense silence hung in the air for a long while before Elizabeth spoke, her voice soft but strong._

"_That isn't your decision to make."_

_Radek retracted his hand, his angry stare still drilling into her._

"_Go back to the lab." She wouldn't meet his eyes. "Prepare for the arrival of the ZPMs."_

---

Sora's bare feet made no sound on the cool floor of the hallways. Darkness surrounded her like a chill mist as she slinked onward. It made her feel almost as if she was the only one in the city. It was a ritual. Since the siege, she'd grown to love it, every moment of it. Just her and Darkness.

Darkness didn't care about all the people she'd killed throughout her life. It didn't care that she'd betrayed her people, or that she hadn't stood up for what was right recently when it mattered most. It didn't even care that she'd made the right decision betraying her people, and it definitely didn't care that she'd returned a lost soldier. That made it a lot easier. If Darkness didn't care, then it didn't ask, and it didn't remind her.

But tonight, Darkness felt like a frigid mist on her shuddering, exhausted body. The comfort of the night had escaped her and left her unable to distract her mind. She wrapped her arms around herself and walked onward, her shoulders heavy.

Coldness washed over her in waves, but instead of covering her sparse workout shirt with the jacket she'd brought, Sora walked on, embracing the sting instead. She needed the reminder that she was still human. Lately, it didn't seem like she was.

Her only contact with anyone on Atlantis was with Carson, and they hadn't spoken much since their argument upon Rodney's return. Since then, she'd gone back to the Genii a few times to continue her charade as a member or their people. Rodney's disappearance was a deep secret, just as his imprisonment had been, but she heard whispers of frustration and anger at the highest level. Somehow, she'd begun to feel more at home back in the Genii homeworld, lying through her teeth as a meager sentry guard, a station given to her as a punishment for her betrayal, than here on Atlantis. The numbness in the pit of her stomach seemed to be the only emotion she could feel. Even when Rodney began to integrate into Atlantis again, her smile didn't quite reach her heart.

Sora was jolted out of her thoughts by a loud scream. She was already turning toward the sound of the noise when the yell faded. Her feet slapped the ground, and she located the room as a second scream lit the air. It was definitely a male. Sora hesitated at the door for a moment. He was probably having a bad dream, she reasoned. He'd awaken himself eventually. What right did she have to barge into his room? Many people still had a problem with her presence on the base – what if this was one of them?

"I won't tell you…"

She was close enough to hear the strained mumbling, and she recognized the voice as Rodney's. Her hand shot to what she'd come to think of as the Ancient doorknob, and the doors slid open. He was lying in a small ball, the size of the bed nearly dwarfing him. The covers had slid to the floor, and she noticed him shivering as she approached.

"I won't…I swear I won't…"

His lips continued to move, but no sound came out of them. Pity stabbed into Sora's stomach as she crossed to his side of the bed. She knew better than to touch him and instead knelt by him.

"Rodney," she said, her voice loud but gentle. "Rodney, you're having a nightmare."

His eyes moved wildly back and forth underneath his eyelids.

"Listen to my voice," she slid her hand beneath his limp one. "You're on Atlantis. You're not in the cell."

A small whimper fell from his lips. "Come on…" she whispered. "Your name is Rodney McKay. You're a scientist from Earth."

His eyelids flickered.

"Your people saved you, Rodney. They took you from the cell. You're okay. You're not there…"

She felt a light squeeze on her hand before his eyes finally opened. Sora sighed with relief, and put her other hand on top of his. A small amount of moonlight flickered in through the window, but she couldn't see his face. She wasn't sure she wanted to.

"I…I'm sorry," he murmured.

She could see that he was slowly regaining himself. "It's all right," she replied.

"No, I…" he paused, looking at her.

"Sora," she told him, knowing what he'd been about to ask. "I know you probably don't remember. That's okay."

"I remember." It surprised her. "You saved me."

The way he said the words, with such gratitude, nearly broke her heart. He sat up slowly, eyes still locked on her silhouette. She picked up the blankets that had fallen to the floor and passed them to him.

"Thanks," he put one over his lower half. "I, uh…" Embarrassment was filtering into his words.

"You're fine. I heard you and I thought I'd wake you up," she stood and pursed her lips. "It's nothing to worry about. Go back to sleep. We all have nightmares here."

Rodney said nothing as she walked back toward the door. Just before it, she stopped and looked back to him. "Rodney?" her voice trembled.

"Yeah?"

"Don't…don't believe them," tears pricked at her eyes, and she struggled to push them back. "Don't ever let them convince you. You're not a number. You're Rodney McKay."

There was a long silence before he spoke. "What are you?" he replied softly.

Her throat felt large and swollen all of a sudden. She blinked, and a tear rolled down her face. "I'm nothing," she told him hollowly, and walked out of the room.

---

"_We're ready to depart for the other planet," John told Elizabeth as he put the ZPM into her hands._

"_They didn't give you any trouble?" She stared down at the object, watching light reflect off its surface._

"_No guards," John shrugged, readjusting his grip on his gun. "Guess their precious artifact wasn't that precious after all."_

"_Very well," she sighed. "You have a go. I'll go deliver this to Radek."_

_John nodded and turned back to Ford and the assortment of Marines that had joined them. Teyla had chosen to help Elizabeth instead of joining her team to recover the ZPMs. In lieu of what they were about to do, John was sort of glad she had._

---


	11. eleven

"_Three hours until the Wraith reach the atmosphere."_

"_Thank you, Peter," Elizabeth acknowledged, her fingers absentmindedly toying with the earpiece of her radio. Her hand trembled, and she slowly, deliberately, moved it back down to the table. Three hours. She let out a long breath. John and his team were two hours overdue. Elizabeth knew in her heart that something had gone wrong, but she couldn't stomach thinking about it, so she focused her mind on other things._

_Radek had been fervently working on the ZPM they'd recovered, but progress had been slow at best. Elizabeth hated questioning him so frequently about progress and pestering him, but anxiety ate at her. She glanced at her clock, reasoning that it had been three hours since their last check in._

"_Radek, it's Elizabeth," she spoke into the radio. Some part of her inwardly cringed, waiting for a harsh tone in his voice._

"_I was just about to radio you," his voice was strained and tired. "Like I predicted, the ZPM will only give us a little over a week of protection with the Wraith firing down upon us."_

"_That's really it?" Elizabeth questioned, desperate._

"_Ano," Radek replied, the foreign word tight with frustration._

"_Isn't there some way to extend that period?" Elizabeth rubbed her temples._

_If only Rodney were here._

_The idle thought struck her suddenly, as powerful and wrenching as a blow to the skull. Her shoulders slumped, her erect form crumbling to a defensive position, as if she could block the agony of her loss._

"_Perhaps I could, if we only extended the shield to certain parts of the city…" Radek continued to speak, but she hardly heard him._

"_Do what you can," she said softly, and took the radio out of her ear, setting it on the table. Elizabeth put her face in her hands and sighed heavily. Exhaustion pressed down around her, but she fought it stubbornly. Regardless, her eyelids slowly flickered shut, her body aching to catch a sparse few minutes of sleep. The sound of her radio crackling to life jerked her out of her doze, and her hand immediately shot out to grab it._

"_We have an incoming wormhole, Elizabeth."_

_She'd never been happier to hear Peter's voice. "I'm on my way. Has any IDC come through?" Elizabeth questioned quickly, as she stood._

"_No."_

_Her feet carried her across the few meters to the control room. She squeezed Peter's shoulder briefly before turning toward a nearby laptop monitor, waiting for an IDC to appear. A long, hopeful silence stretched over the room before it finally beeped._

_  
"It's them!" Elizabeth cried with relief. "Lower the shield!"_

_She nearly flew down the stairs as the wormhole was established and the shield fell away. After a moment, a few scraggly looking children and teenagers began to appear, looking around the 'gate room with a mixture of fear and wonder. Usually, Elizabeth enjoyed watching the reactions of newcomers, but she hardly glanced at them today. She only wondered where her team was and why there were so few refugees._

_Finally, familiar faces straggled through the horizon. Elizabeth's heart was in her throat as she saw two Marines approach, a third on a makeshift stretcher between them, an arrow sticking out of his chest. As they came closer, she identified him, a pang of sorrow hitting her._

"_Med-team to the 'gate room," she said quickly into the radio, her eyes on the man's ashen face. A few more men came through the 'gate, scratches and bruises marring their visible skin, and then, bringing up the rear, came Aiden and John. John passed a black bag to a fellow soldier, instructing him to take it to Radek, and immediately sought out Elizabeth as everyone else dispersed._

_Elizabeth felt a tendril of horror touch her as John approached. An ugly bruise stretched from his neck to his jaw. She wondered what kind of blow would cause such quick damage. Her eyes assessed the bloody cut on his forearm, and through her swirling stomach she guessed that it was a knife wound._

"_What happened?" she said softly._

_John hesitated._

_Elizabeth couldn't take her eyes off of the wound on his arm. It reminded her of the deep cut on Rodney's arm when Koyla had tortured him. She wondered briefly if that had been just the beginning – was Koyla torturing him, even now? Nonetheless, she couldn't afford to wonder, and instead forced herself to focus on John's words._

"_They didn't want to leave their home and denied us use of their ZPM," his eyes were cold as he spoke. Elizabeth remembered that look on his face, and kept silent, wondering in silent terror what had occurred. "We went to the shield generator to steal it, but they'd posted guards."_

_Guards, Elizabeth thought. More like small children wielding arrows and spears._

"_We neutralized them, but they managed to sound an alarm. Simmons and Trace decided to go door to door and collect any people wanting to come with us. Trace got an arrow in him – Simmons carried him from the village to the 'gate as they were being chased. The–" John hesitated briefly, "the soldiers caught up with us by the 'gate. There was a fight."_

_Elizabeth's eyes settled on the retreating backs of the Marines and placed herself in their shoes, murdering their allies – just children, really – to get the ZPM because she'd ordered them to._

"_I'm sorry, John. But you did good," she told him, trying to tell him in her undertones that what he'd done was right. "You should go see Beckett," she added._

"_Beckett has more important things to do," John dismissed. "I'm going to go help Radek with the weapons system. He needs someone with the Ancient gene." Without waiting for her reply, John walked away._

"_John!"_

_He turned, raising an eyebrow._

_Elizabeth hesitated as she realized that John didn't want to talk about it – not now, and probably not ever. "We…we have just over two hours," she told him finally._

_John nodded and walked away._

---

When Elizabeth entered the control room, she found it completely empty, with the exception of Rodney McKay. It wasn't too odd that the room had been deserted – outside, the sun was grazing the horizon, and most of the expedition members were probably eating dinner. She guessed that Rodney had relieved Peter of his command, and stepped closer, shifting the data pad back and forth in her hands.

Rodney was staring at one of the consoles, a faraway look in his eyes. Elizabeth smiled briefly as she approached him.

"Hey, Rodney."

He lifted his head slowly, lost blue eyes finding hers slowly. Elizabeth furrowed her brow, her gaze darting downward to see the fingers on his right hand trace over the skin on his opposite arm. A lump formed in her throat as she stared at his left forearm. She remembered too clearly being dragged from this spot, Rodney's yells echoing through the room –

"I remember," he said softly, carefully.

"Rodney-" she took a step closer, but he immediately moved backward. For the second time, Elizabeth's eyes fell on his arm. Even with all of the new scratches, bruises, and scars Rodney had developed, the white, straight line on his skin was nearly luminous.

"I gave him the information he wanted," there was a vague note of disgust and disappointment in Rodney's voice, and Elizabeth felt a tug on her heart.

"He _tortured _you," she stepped forward again, this time boldly putting her hand on his shoulder. "It wasn't your fault. And it ended up all right in the end, didn't it?" she attempted a smile, but it slipped off her face quickly.

"We made an enemy out of the Genii." Rodney's words were deliberate and succinct, something that Elizabeth was quite unfamiliar with. "And that's probably why they took me. Because they thought I would tell them what they wanted."

She didn't know what to say to that, so she just told him the first thing that came to mind, her voice soft.

"They were wrong, Rodney. You were so brave," she fought to keep her composure. "They tortured you for hours, for days, for months. And you still held on. You never told them anything. I don't know if I could count on _soldiers_ to do that, much less scientists. When you were gone… We all did some things we aren't proud of; some things that we promised ourselves that we wouldn't. You're the only one that stuck to what you believed in, and…" she swallowed tightly, fighting the tears building in the back of her eyes. "I'm so proud of you, Rodney." Her cool hand reached out to touch his face, as if to reassure herself again that he was really there. "I'm so proud of you for withstanding that nightmare. You're one of the strongest people I know. I wish I could be like you. Strong. Unwavering." A shaky smile appeared on her face.

Rodney smiled slightly, and Elizabeth could tell her words had sunk in. After a moment, he turned back to the console. "The memories… They seem like they just happened."

"How much have you started remembering?" Elizabeth asked, curiosity in her voice.

"Lots of things. Experiments, missions, people…" he paused, "some of the things they did to me in the prison."

"Is it hard?" The curious question spilled from her lips before she could stop it.

Rodney hesitated. "A lot of times…yeah."

Elizabeth slipped her hand into his open palm and squeezed it gently. "I'm sorry. But know that I'm here to help you bear the burden."

He squeezed her hand in return. "The same to you," he said softly. Her sorrow hadn't gone unnoticed by him. As his words reached her ears, he saw it again: the brief, quickly masked flash of pain across her face that told him more than anyone would reveal. Something had happened in his city in his absence – something that had left Elizabeth hurting nearly as much as he was hurting.

Her forced smile was distant and cold now. "Well, hopefully you won't have to do that for a while," she told him. He knew her nonchalance was pretend, and didn't bob his head and continue with their conversation like she was obviously hoping.

"What happened here?" Rodney finally questioned. But it was much too soon – Elizabeth's hand fell from his and she took a small step backward, shaking her head slightly. He sighed in disappointment. "Elizabeth–"

"Just focus on getting better, Rodney," Elizabeth told him, again with the plastic smile, before turning and walking away.

Of the many memories that had begun reappearing in Rodney's mind lately, the strongest were those of his period of torture, the times when he sat alone in his cell, hanging on the edges of his sanity. He remembered clinging to the image of Elizabeth in his mind, and how thoughts of her kept him from breaking down.

He'd forgotten it once, but he would never do it again. Unbeknownst to herself, Elizabeth had kept him from giving up hope, from telling his captors the information they sought, from killing himself to stop the pain, and so many other possible outcomes. He owed her his life.

And that was why Rodney was so determined to find out what nightmares were plaguing her. She was helping him overcome his memories, and he would do the same for her.


	12. twelve

**Author's Note: **So it's been what, five months? Wow. But it's nearly summer vacation now, so hopefully I will actually have time to write. :) Hope you guys enjoy, and a big thank-you to **fififolle **for the generous beta.

---

_It had been two weeks, Rodney told himself, running his fingers over the carvings of fourteen short, rugged lines on the far wall of his cell. He could be wrong, of course – the small window at the top of his cell never showed anything but black, leading him to the assumption that he was underground, and there were no real indications of days passed. On what he assumed was every morning, two guards would come and put a small pail of water and a piece of stale bread inside his cell and walk away. He carved immediately after that, holding on to the hope each line gave. Atlantis would be organized now…they would be searching…every hour searching was an hour closer to him… But with hope came doubt. The longer he was here, the less likely he was to remain alive, the less likely it was that every resource in Atlantis was being dedicated to finding him. He tried not to think of the pending Wraith attack on Atlantis, telling himself that he would return to the city in time to save them. Or maybe Atlantis had already beaten the Wraith. He wished he knew._

_Rodney reminded himself that time was relative as he let his hand fall to his side. It seemed like he'd been here for years. A small voice in the back of his mind asked him what it would feel like, then, when he had been here for years. Stubbornly, he pushed the thought away, refusing to give in to the thought that his saviors would never come. It was due to survival more than his faith in his friends._

_There was a stirring across the hall. Rodney lifted his battered body and hobbled toward his bars, no longer cringing at the layer of rust and grime covering them. The day before, two men he didn't recognize had come and placed a new prisoner into the cell directly across from his._

_Rodney reminded himself with disgust that at least his own presence behind these bars was understandable. It was one thing for them to capture a grown man, to torture a knowledgeable enemy – but this was different. Rodney was beginning to understand just how twisted the Genii really were. Their new prisoner couldn't have been more than eight or nine years old; a blonde-haired, fragile little girl. Anger boiled in the pit of Rodney's stomach. Until now, she had remained unconscious, small body huddled on the cold concrete of her cell. Rodney thought of all of the pain he had withstood since his arrival and stared at that little girl, wondering what they would to do her. What could she have done? He already knew the answer. They were Genii. They would do anything to get what they perceived they needed. She, tiny little vessel that she was, had some use, some information._

_Wincing at the aching in his back, Rodney crouched down, touching the ground to steady himself as he slowly watched the girl come to. He knew fear when he felt it clutching him and he knew it now as it reflected in her blue eyes. Her hands turned into tiny fists, chest heaving with every quick breath. Rodney waited patiently. Eventually he moved to sit down, keeping his eyes on the girl. Her panic rose, then subsided, and after realization began to settle in, her eyes finally found his. Their cells were only six or seven feet apart, but the bars made it seem like six or seven continents. Rodney glanced down at his hands for a moment, rubbing his fingertips over the collection of bruises and scabs before looking up again. He knew that nothing he could say would comfort her – but he also knew that being in contact with some other person might. So, out of some inward obligation he perceived he had, Rodney attempted to start a conversation with her._

"_Hey."_

_The girl looked at him with wide eyes, wary and frightened. Rodney tried again, remembering how he had awoken two weeks before, aching, confused, and alone._

"_I'm Rodney." It was a phrase he consistently repeated to himself out of fear that he'd lose it, but it took a different meaning now. The girl shifted slightly, drawing closer to the sound of Rodney's voice._

"_My name is Amaya." She tilted her head, surveying him. Rodney, in turn, took in the bruise on the side of her forehead. "Are you lost, too?"_

--

It had been a month since John and his team had returned to Atlantis, Rodney McKay's limp, battered body among them.

Elizabeth mulled over that fact for a moment as she walked through the hallways of Atlantis, data pad in hand. As she approached the infirmary, she heard the sound of laughter as it drifted through the doorway. She smiled and continued into the room, spotting Rodney and Sora sitting next to each other on the infirmary beds and Carson standing before them. Elizabeth paused where she was, taking in Rodney's appearance.

The bruises had begun to fade, as well as the cuts and the burns. Carson had finally let Rodney out of the wheelchair and onto crutches, and eventually off those, too, but only after Rodney promised to use a cane. Rodney, in return, had been "misplacing" the cane anywhere he could, much to Carson's annoyance. But even behind Carson's frustration, there was relief and happiness. Rodney's presence on Atlantis had seemed to have a remarkable healing affect on the population – it wasn't just here that Elizabeth was hearing laughter again. Maybe it was sinking in for everyone that if Rodney, the man with the most nightmares in this city – maybe even this galaxy – could overcome what he'd been through and move on, so could they.

"Are you going to come in or just stand there?" Sora's voice jerked Elizabeth out of her reverie.

"Sorry, I lost myself there for a moment," Elizabeth said with an easy smile, walking into the room. Carson and Sora knew what she'd been distracted by as easily as if Elizabeth had spoken her thoughts aloud, but neither of them said a word about it.

"Rodney is coming along well," Carson announced, patting his friend on the shoulder as he did so. Rodney was used to the overabundance of affable gestures by nearly everyone on Atlantis. He understood that sometimes they needed to touch him to remind themselves that they weren't dreaming; that Rodney really was standing in front of them, alive and well.

"Carson and I were just talking about restarting training," Rodney told her. Elizabeth froze on the spot, hoping the sudden fear that clenched her didn't bleed through her smile.

"I told 'im maybe in another week," Carson answered the unspoken question.

It seemed like Rodney had just shown up yesterday and today he wanted to go back off-world, to leave her again. Elizabeth swallowed her feelings, but not before Rodney picked up on it. Of all the things she wished had stayed forgotten, it was his ability to read her.

_Worry about it later,_ Elizabeth told herself and quickly turned the conversation towards less dangerous topics. She felt her body relax in this familiar banter.

"Carson, you're on your lunch break now, aren't you?" she questioned suddenly.

"Aye."

"Well, then, how about we all go grab some food in the commissary?" Elizabeth proposed with a smile, looking at each of them. Not for the first time, she thought of how lucky they all were. It seemed like time for a celebration.

--

_Elizabeth tried to conceal the trembling of her limbs by leaning up against the doorway, arms folded across her chest as she watched Radek push the newly acquired ZPM into place. A couple of hours ago, she'd been able to convince Carson to give her some stimulants. After nearly falling asleep in her office chair, she had made herself a cup of coffee and set about checking up on everyone. Between the coffee, lack of sleep, and the stimulants, she was nauseated and suffered a pounding headache, but she did the best to put it out of her mind._

_Radek moved to his laptop, pressing keys and hoping against all hope. But they all were, weren't they? This broken city was no match for the Wraith. He continued typing. A diagnostic began to run and as it did so, Radek looked at his fingers, for a moment imagining the blood of children staining them. He caught Elizabeth's gaze and looked away quickly, unable to hide the mix of anger, sympathy, and revulsion he had for her. Perhaps she sensed it – her impatience was gone from her face for the moment, her lips sealed against small talk._

"_The ZPM is severely depleted, as I feared," he told her, assessing the data as it began to appear. 'I told you so' ran underneath his words._

"_How much time did it buy us?" Elizabeth asked, her voice oddly empty._

_Frustration, exhaustion, and fear claimed Radek again and he snapped a reply. "You don't get it, do you?" his accent was heavy with anger. "It doesn't matter how much time we can buy. The Wraith will wait us out. A couple of hours or a couple of days or maybe even a couple of months if we are lucky – the shield will fall and they will kill us all."_

_Silence followed his words. They were the bare truth._

_Elizabeth met his eyes, understanding his anger and knowing only a part of it was directed toward her. A large part, but a fraction all the same. "We have an hour, Radek. Do you have another plan?" She paused briefly before continuing. "Look, I know it won't save us. But if we have just a little bit of time…we'll find a way."_

"_Too many have already died for us not to," Radek stated. Elizabeth clenched her jaw but said nothing at the hidden barb in his comment. He sighed and turned back to his laptop. "I'll see what I can do with what power is left in the ZedPMs but-"_

_He stopped abruptly and Elizabeth froze._

"_I…I'm sorry. He said it a lot, and I—"_

"_No need to be sorry," Elizabeth cut him off with a strained smile. She knew that Radek was missing Rodney now, too. "Just…keep trying."_

_Elizabeth left the room as shaky as she'd come, running her fingers along the wall. 'Ten thousand years,' she thought, 'you've survived. And I'll be the one to give you to the Wraith.'_

---


	13. thirteen

**Author's Note: **Life has been crazy. My apologies for the lack of updates, but hopefully that changes.

**---**

For the first time since he'd returned to Atlantis, Rodney McKay was alone in his lab. Nearly ten minutes ago all of the other scientists had headed toward the commissary for lunch. Rodney had declined the invitation, telling them that he was going to continue with his work instead. His excuse was only halfway true, but they had believed it, as he knew they would. Lately, the times when Rodney wasn't catching up with his teammates, he was working. As happy as he was to be home, the subtle pressure bearing down on him to 'go back to normal' was too much to handle twenty-four/seven. Working provided an escape. Engrossed in his experiments, he barely noticed that he could now remember almost every bit of research he had done on Atlantis. With that came more memories – memories of missions, of invasions, of space battles, of happy conversations, but also of things better left forgotten. Rodney had yet to decide whether it was a good or bad thing, but he felt he _should _know.

But today, he closed his laptop and rolled away from the table, tucking the computer beneath his arm as he did so. After a quick peek around the hallway to make sure none of his fellow scientists were around, Rodney stepped out of the room and began a speedy walk away from the lab. There were questions he had that needed to be answered – and no one here seemed to be willing to do so. He brushed his hand against an Ancient panel and slipped quietly into a room. The door shut quickly behind him.

It was a small room that Rodney had discovered more than a year ago. 'Room' was a little too generous – it was more of a large closet than anything. A monitor, an Ancient console, and a chair from Rodney's quarters were all the room contained. With a grim smile, Rodney sat down and set his laptop down gently by his feet. He had used this place often, but he kept the location to himself. The only computer that had access to the entirety of the Ancient database was the computer in the control room – and this one. Rodney supposed it was a safety measure in case the first was destroyed or invaded (which would've been helpful back when Koyla started his invasion, Rodney thought bitterly, wishing he had discovered it sooner). Even the small thought of a Genii made his muscles tense and he slowly forced himself to relax, setting his fingers on the console. The room had allowed Rodney to work through a chaos in silence several times – and once again, he called on it to help him.

The more that he remembered about Atlantis, the more he realized that things were _different_. He knew his absence was not the cause. From experience, he knew that loss brought the expedition even closer together. But he had returned to a splintered Atlantis. Everyone seemed to branch away from each other, as if there was some contagion in the population. John was abnormally reclusive, Elizabeth dined alone nearly half the time, Kate was often too busy with appointments to see Rodney for anything other than work purposes, Aiden and Teyla spent a majority of their time on the mainland… Even Rodney, normally so oblivious to people's emotions, could tell that, beneath their struggle to carry on with their everyday lives and to welcome him back, things had changed. People were angry, depressed, resentful, horrified…and no one would speak of it. Rodney's curiosity had driven him here, the one place where he could access every file in existence on Atlantis in private, the one place he could find his answers.

Rodney started with mission reports. Summaries filled the screen, and a particular one caught his eye.

**Mission ID: **PQ20165-5  
**Mission Status: **Failed  
**Comments: **Rodney McKay still MIA. No further information obtained.

A knot formed in his throat as Rodney stared at the reports that filled the bottom of the page. _**Mission Status: Failed**_blinked vibrantly next to each one. Elizabeth had told him that they had looked everywhere for him, but now he could see the true scope of it. For a moment, he forgot his purpose, scrolling through the countless planets they'd searched, the favors they'd called in, the leads that went nowhere…

With a tight swallow, Rodney scrolled to the more recent reports, refocusing on what he had come here for. He read through the page and was surprised to find that, since the two reports that he guessed had occurred during the Wraith attack, there were only a few reports. Why weren't they exploring other planets? An apprehensive feeling trickled through him. Subconsciously steeling himself for what was to come, Rodney gazed at the reports from the siege.

**Mission ID: **PQ20165-7  
**Mission Status: **Completed  
**Comments: **ZPM acquired.

He paused for a moment. _PQ20165 _- he would recognize that number anywhere. He pushed away the sharp memory of his kidnapping, instead thinking of the ZPM the planet had on display. AR-1 had been negotiating for the ZPM, Rodney recalled. Had the negotiations succeeded after he left? _Acquired._ Something told him that Atlantis had tired of negotiations. Had the impending threat of the Wraith been enough for them to steal a ZPM? Rodney could imagine John's angry voice in the briefing room, exclaiming, '_They just use it for decoration! We're at __**war**__!'_ Rodney's eyes moved onward.

**Mission ID: **PQ00025-54  
**Mission Status: **Completed  
**Comments: **Natives hostile. Few refugees taken. ZPM acquired.

It took a while for his brain to digest it. The implications of the three lines of text sunk into his skin slowly, like a poison. He could try and pretend not to remember, but he knew all too well what planet PQ00025 was. The first time they arrived, they were having ritual human sacrifices of each person who reached the age of twenty-five. After that, they'd made several trips back. Rodney, Elizabeth, and Radek had been the most frequent visitors.

_ZPM acquired. _Rodney's heart pounded in his chest as if it was a crisis he could stop. The kids needed the ZPM for the shield. They were _safe_ from the Wraith with it. Why had Atlantis taken it? _Few refugees taken. _Had they really been so desperate for ZPMs, for power that they would resort to this thievery? _Natives hostile. _The phrase repeated over and over in his mind. Two words made his blood run cold. He had seen that written on several summaries of missions he'd participated in. It meant bloodshed, death, guns, running for life… But they were just _kids _on PQ00025. There weapons weren't much more advanced than a slingshot. It was obvious who would have won a fight between the kids and the marines of Atlantis. But _why _would they fire on innocents?

The kids had tried to stop them.

Rodney could picture what happened now, the imagined scenes running through his mind. He thought of his two companions – he grimaced to call them friends – who accompanied him to the shield generator every time he visited. Were they here? Or had they been gunned down by a marine? There was just one line below the two entries before the summaries entered a pattern of treaty-negotiating and crop retrieval but little else.

**Event Update**: The Wraith vessels attacking Atlantis have been destroyed.

A loud burst of static and indecipherable speaking broke the silence. Startled, Rodney glanced around before realizing that he had left his radio earpiece on.

"What was that?" he questioned, too shocked by what he had discovered to sound as snappish as he had meant to.

"McKay, are you there?" it was definitely a girl's voice.

"Yes?" Rodney leaned back in his chair.

"It's Sora. I, uh…" she hesitated for a moment, and began again. "Whenever you've got a free moment, could you come and see me? I want to talk to you. I'll be in my quarters."

Rodney frowned at the odd request, but replied, "Alright." He glanced at the monitor briefly before standing up and picking up his laptop. If there was more to learn through snooping, he wasn't about to find out today. "I'm on my way," he said into the radio, and then turned it off. If there was an emergency, they could reach him in other ways. For now, he wasn't sure that he wanted to talk to anyone. He thought for a moment about radioing Sora and telling her that he was too busy, but the way that she had talked to him made it seem like there was something important she needed to tell him.

Maybe it had something to do with all of this, he thought grimly as he left.

---

"_Sixty-Two."_

_Rodney looked up wearily at his name, bloodshot eyes glaring up at the two men entering his cell. "I have a name," he corrected them, his voice tight. It's going to take more than three weeks to break me, Rodney thought, hatred burning through every inch of his flesh, a canvas bright with the reminders of the brutality of these people. Still, he felt dread and hopelessness churning in his stomach wildly as he sat. He could do nothing but bear the wounds they gave him and resist._

"_You are little more than nothing. You are a number, a means to an end." Their voices sounded hazy, like the words had traveled through water before they reached Rodney. Lines of dry blood ran from his ears down to his neck, a testament to the damage the two had dealt him the day before._

"_A means to the end of Atlantis and the end of suffering for your people," Rodney mused, letting his head rest against the concrete wall. His captors stayed toward the other end of the cell for now, shadows covering their faces. "I'd say that's a lot more than nothing." He prepared himself for the blow to punish his insolence, but it never came._

"_When will you break, Sixty-Two? I tire of this game," First interrupted. "Atlantis fights the Wraith as we speak. They have stopped searching for you. You are dead to them; dead to the world. Rodney McKay exists in their memories and you, Sixty-Two, will never exist anywhere but this cell."_

"_You didn't expect me to keep your little nickname once I'm free, did you?" This time the blow did come: a hard backhand into his already bruised cheek. Rodney spat the blood in his mouth and faced them again. He remembered sitting in a cell with John, silently panicking as John spat insults at their captors. But now more than ever he understood why John did it. They had to use the only tools they had available to fight back because not to fight was to lose; to lose everything._

"_How is little Amaya these days?" Second questioned abruptly, glancing over at the cell that housed the sleeping child._

"_I wouldn't know," Rodney replied evenly, his eyes locked onto Second's._

"_But you guys are real buddies now, aren't you?" Second questioned. "We know you've been talking to each other, Sixty-Two." Rodney said nothing. Inwardly, his heart leapt against his rib cage for fear of what the monsters would do if they set their attentions to her. His worry was well-founded._

"_Hit a sensitive spot, did we?" said First. "What's wrong? You look…worried," he continued, sneering._

_Rodney was silent once more. It was one thing to rebel when the punishment would be dealt to him alone; it was quite another to do so when someone else had to pay the price. He watched Second pull a short metal rod from the belt at his waist, twisting the object in his hands while he spoke. Rodney touched the side of his jaw softly, knowing that the rod's shape was still imprinted in deep purple hues there from days ago._

"_Do you know why she is here?"_

"_No," Rodney answered honestly. He knew that she had been wandering in a marketplace, having lost track of her mother, when she was kidnapped. He knew that she loved and missed her doll Tracy and he knew she was confused and scared. He knew that the fact she was even in this cell made him want to rip out the throat of every Genii he could lay his hands on._

"_Her father was an enemy of Cowen's administration." It was a new voice this time, from out of the cell and beneath the dim, hanging lamps. Rodney's eyes shot to the outline of the man, nausea rising in his stomach. The voice was familiar – terribly familiar. The man stepped from the shadows into the light by the entrance to the cell and finally Rodney could see his face. "Hello, McKay."_

"_Kolya." Though his scraped and bruised hands protested, Rodney pushed against the ground and managed to stand, leaning against the wall slightly to support himself._

"_I am glad to see you doing well," Kolya said with a smile as First opened the cell door. "I would hate for our time together to be short and painless."_

"_Yes, well, wouldn't that just be horrifying," Rodney answered numbly. The door slammed shut and he jumped at the loud, harsh noise. After a pause, he spoke again. "So you're the one behind this."_

"_I always liked you better than Sheppard," Kolya said, ignoring Rodney's statement. He clasped his hands behind his back and strolled back and forth in the cell. Rodney's eyes fell on the gun holstered at his hip. "You always knew the odds; knew how to reason. Sheppard…Sheppard would hold fast to his military training no matter what the stakes."_

_At the mention of John's name, Rodney felt a surge of emotion in him. Sheppard __**is**__. He was alive. The Wraith hadn't attacked yet. Or better yet, maybe they had. Maybe Atlantis had won without him. Maybe now they could devote time to search for him…_

"_I am about to appeal to your sense of reason, Dr. Rodney McKay." Kolya stopped his pacing and faced Rodney. "I have no use for this child," he gestured toward Amaya. "Her father was staging a rebellion against Cowen. He and his rebellion are dead now. I have two choices here. I can make her an example for others or I can send her back to her mother."_

_The nausea that Rodney had felt upon Kolya's arrival was now back in full force. First and Second had proven themselves adept at pain and misery, but Rodney knew Kolya's potential. His eyes couldn't leave the gun, remembering when its muzzle had been pointed to Elizabeth Weir, Kolya's finger closing on the trigger… He remembered the knife digging into his forearm, Kolya's voice but a whisper in his ear as he told Rodney all of the things that would happen to Elizabeth if Rodney didn't give in._

_Kolya knew how to break people. Not for the first time in three weeks, Rodney was terrified._

"_I want the code to your iris, McKay."_

"_I won't give you anything," he replied firmly, locking his jaw and closing his trembling hands._

"_Because withholding information is such a strength of yours," Kolya said, his voice dripping with sarcasm, the emotionless smile curling around his lips again. His dark eyes met Rodney's. "I am about to give you a choice. Either you give me the code and I let her go home or…" he moved his gaze toward the other cell._

_Panicked by Kolya's presence, Rodney hadn't noticed Second slipping outside of the cell. But now he watched the other man open Amaya's cell and step into it. He knew what Kolya was insinuating._

"_No," the whisper left his lips without him even realizing it. Kolya took a few steps forward until he was within inches of Rodney._

"_She is innocent, McKay. So very sweet…pure… But things will be done to her that make you prefer death over observance if you do not give me what I desire," Kolya placed his hand on Rodney's shoulder, digging his thumb into a bruise relentlessly. Rodney winced and let out a small groan of pain. "I will give her back unharmed to her mother. You have my word. I have no use for her. Just tell me the code."_

"_I can't," Rodney replied, horror thick in his throat. He felt every bruise, every cut, every scratch on his body. Was that what awaited Amaya?_

"_Look at her!" Kolya's hand roughly grabbed his face and turned it to the girl. She was laying in the corner, blonde hair fanned out around her face like a halo. Her face was settled peacefully in sleep, her body curled into a small ball. "Imagine what I could do. What I will do."_

_Rodney's heart thundered in his chest. "Don't do this, Kolya…"_

"_I must save my people, McKay. If you believe in yours, then they will have no trouble defeating me. Save her. Give me the code."_

_Amaya's eyes fluttered open. From yards away, Rodney could see the panic slowly settle in her eyes as she fully awoke and saw Second standing in her cell. The door slammed shut behind him._

"_Fine. Fine! It's 2673 Alpha—"_

_Kolya backhanded Rodney, sending the other man spiraling to the ground. "You think I am stupid, McKay?!" he sent his boot flying into Rodney's abdomen. "I know your panic code." He dragged Rodney to his feet by his tattered jacket. "Second!" he called to the other man._

_Second's eyes went toward Kolya. Again, Rodney's eyes were drawn to the metal bar in the man's hands._

"_No," Rodney squirmed against Kolya's grip. "No! There's another way… Don't do this…"_

"_Tell me the code, McKay, and I'll let her go."_

"_I can't… I can't…" the words were a faint whisper._

_Kolya nodded to Second, who drew the bat back and advanced on the girl. She clambered back farther into the corner, bringing her hands up as if to defend herself._

"_NO!" Rodney cried, throwing himself at Kolya. They hit the floor as Amaya's shrill scream lit the air._

_---_


End file.
